The opinion of the court was delivered by: James Robertson United States District Judge
Plaintiffs Legacy Fishing Company and Fishing Company of Alaska, Inc. have filed suit against Commerce Secretary Carlos Guitierrez in his official capacity challenging the legality of Amendment 79 to the Bering Sea/Aleutian Islands Groundfish Fishery Management Plan and its implementing regulations. Environmental organizations Alaska Marine Conservation Council and Oceana have joined the suit as intervenor defendants . Plaintiffs allege that the amendment, which was designed to reduce the incidental capture of unwanted fish by commercial fishing vessels in the region, violates the Administrative Procedures Act and the Magnuson Stevens Act (Counts I - IV), and the Regulatory Flexibility Act (Count V). All parties have moved for summary judgment , , . For the reasons discussed below, defendants' motions for summary judgment , , must be granted.
Plaintiffs operate commercial fishing vessels off the coast of Alaska in the Bering Sea/Aleutian Islands ("BSAI") region. Legacy Fishing Company is an Alaska corporation that owns and operates F/V Legacy, a 132-foot vessel. Fishing Company of Alaska ("FCA") is a Washington corporation that operates six larger vessels. F/V Legacy targets high quality, low volume groundfish such as rock sole, rex sole, and Pacific cod, mostly for sale in the Asian restaurant and sushi markets.  ¶ 17. The FCA vessels harvest Atka mackerel, yellowfin sole, rock sole, and rockfish in a very high volume fishery.  ¶ 19. These vessels are part of the "Non-AFA"*fn1 , or "H&G CP"*fn2 sector of the commercial fishing industry in the region. The H&G CP fleet moves between fisheries throughout the year in pursuit of a wide variety of fish, unlike the AFA fleet in the region, which primarily targets a single stock (pollack). Plaintiffs stress that they are entirely dependent upon the North Pacific groundfish trawl fishery.*fn3  ¶ 5, 6.
The parties agree that no species of fish in the BSAI groundfish fishery is "overfished" or "subject to overfishing" as defined by the Magnuson-Stevens Fishery Conservation and Management Act ("MSA" or "the Act").*fn4  ¶ 5. Whether or not there is overfishing, however, the MSA expressly declares that is it the "policy of Congress . . . to assure that the national fishery conservation and management program . . . encourages development of practical measures that minimize bycatch and avoid unnecessary waste of fish." 16 U.S.C. § 1801(c) (emphasis added). "Bycatch," as defined by the MSA, includes "fish which are harvested in a fishery, but which are not sold or kept for personal use, and includes economic discards and regulatory discards." 16 U.S.C. § 1802(2). Economic discards are those fish caught by a fishery but "not retained because they are of an undesirable size, sex, or quality, or for other economic reasons"; regulatory discards are "fish harvested in a fishery which fishermen are required by regulation to discard whenever caught, or are required by regulation to retain but not sell." 16 U.S.C. §§ 1802(9), 1802(38). Excessive bycatch is a problem in the BSAI, especially in the H&G CP fishery, which has the worst bycatch rates in the BSAI. 71 Fed. Reg. at 17,362.
Minimizing bycatch presents more of a challenge to F/V Legacy than to those vessels in the region that harvest a single species of fish (such as the vessels in the AFA sector).  at 4. Because the AFA sector, for example, targets specific stocks in more stable fisheries, its vessels are less likely to catch fish they cannot use. Id. In addition, vessels such as those in the AFA sector, because of their size and specialized equipment, qualify for Coast Guard endorsements which enable them to keep and process certain fish that plaintiffs and others without the endorsement are forced to discard. Id. at 4-5. The difficulty of bycatch minimization also varies within the H&G CP sector, as evidenced by a comparison of the plaintiffs' bycatch rates. F/V Legacy, because it focuses on lower volume fisheries, has much higher bycatch rates than the FCA vessels, which are the largest in the H&G CP sector and concentrate on high volume fisheries. Plaintiffs maintain that, despite these challenges, the H&G CP sector has made significant strides through its voluntary efforts to reduce bycatch using "information sharing, gear research, and development of markets for new products." Id. at 5.
The MSA establishes a comprehensive fisheries management system for the waters of the United States. 16 U.S.C. § 1801(b)(1). Congress's primary goal in passing the MSA was to address overfishing and mandate the sustainable conservation of threatened fish stocks. Id. at §§ 1801(a)(2), 1851(a)(1). In furtherance of this mission, the MSA creates eight regional fishery management councils. Id. at § 1852(a). Members of the regional councils include state and federal government officials and individuals nominated by state executives and appointed by the Secretary. Id. at §§ 1852(b), (c). The MSA charges the councils, in cooperation with the Secretary of Commerce, with developing fishery management plans ("FMPs") for fish stocks within their regions that require conservation and management. The Act details the procedures to be used in developing FMPs and sets forth standards to which the plans must conform.
Under the framework set forth in the MSA, the fisheries in the BSAI region are managed by the North Pacific Fishery Management Council ("the Council") under the North Pacific Groundfish Fishery Management Plan ("FMP") for the Groundfish Fishery of the BSAI.  at 2; 16 U.S.C. §§ 1852(a), (h)(1). In June 2003, the Council adopted Amendment 79 to the FMP. 71 Fed. Reg. at 17362; A.R. 13 at 1. The purpose of this Amendment was to establish groundfish retention standards for the BSAI that would limit bycatch "while maintaining a viable multi-species trawl fishery." A.R. 111-04 at 10. The new groundfish retention standards ("GRS") adopted by the Council in conjunction with Amendment 79 apply only to H&G CP sector vessels measuring longer than 125 feet. 71 Fed. Reg. at 17364; A.R. 13 at 3. All such vessels are required by the Amendment to retain an increasing percentage of the groundfish they catch: 65% in 2008, 75% in 2009, 80% in 2010, and eventually 85% in 2011. Id. Right now, F/V Legacy retains only 48% of the fish it catches; in other words, 52% of its catch is bycatch. Plaintiffs maintain that F/V Legacy will be forced out of business by even the first of these four retention standards (65%), since it lacks both the storage space and market demand for the additional fish. The FCA vessels, on the other hand, already meet the most severe groundfish retention standard (85%), but the FCA has concerns about other changes mandated by the amendment.
In addition to setting groundfish retention standards, the Amendment adopted by the Council in June 2003 also requires plaintiffs to enhance the monitoring and enforcement measures ("M&E") aboard their vessels. Additional "observers" must be brought on board vessels to sample the catch as it moves along a conveyor from a storage tank to the factory of the ship, the vessels must be outfitted with "flow scales" for weighing the fish, and "observer stations" must be constructed aboard the vessels to improve monitoring. A.R. 111-04 at 113-14. In addition, after the Council adopted Amendment 79, the National Marine Fisheries Service added two significant requirements via regulation: (1) a prohibition on "mixing of hauls"*fn5 and (2) a ban on simultaneously running two conveyors from a vessel's fish bin to its factory. 71 Fed. Reg. at 17363, 17374. Plaintiff FCA asserts that these additional "requirements will force Plaintiff FCA to either expend up to $5 million in vessel retrofits or, even more impracticably, halve its production. (A.R. 167 at 7-8, 10-11.)"  at 9.
Plaintiffs filed this suit on May 5, 2006, asking this court to (1) enjoin the operation of Amendment 79 to the FMP;
(2) order defendant to rescind the Amendment 79 regulations that were not recommended by the Council; (3) declare that the final regulations implementing Amendment 79 were promulgated in violation of the MSA, the APA, and the RFA; (4) award plaintiffs costs and attorneys' fees; (5) defer application of Amendment 79 until a proper RFA analysis is conducted.
I. Count I: The Monitoring and Enforcement Provisions Developed by the NMFS
Plaintiffs' first complaint is that certain monitoring and enforcement provisions -- the ban on the mixing of hauls and the requirement for a single flow scale and observation point -- were neither considered nor recommended by the Council in June 2003, but were instead drafted later by the NMFS and were therefore "promulgated in excess of the Defendant's authority."  at 23-24. Additional background on the development of Amendment 79 and its implementing regulations will be useful in understanding plaintiffs' objections.
The regional Council, pursuant to its authority under the MSA, began working on developing a plan to reduce bycatch rates in the BSAI at least as early as December 1994, when it initiated its "improved retention/improved utilization (IR/IU) program for the BSAI groundfish fisheries." A.R. 30-031 at 20. In June 2003, after years of debate over the best way to address the problem, the Council adopted (1) Amendment 79 to the BSAI FMP, which authorized a groundfish retention standard program (GRS) for reducing bycatch, and (2) certain rules designed to implement the bycatch-reduction goals of Amendment 79 and are referred to by defendants as the "GRS program." 71 Fed. Reg. at 17,362. When the proposed rule for the GRS program was eventually published in the Federal Register on June 16, 2005, however, it included two additional monitoring and enforcement provisions that were not among those recommended by the Council in June 2003 -- the ban on haul mixing and the requirement for a single flow scale and observation point.
It is uncontested that it was the NMFS, not the Council, who developed these two additional M&E provisions. In fact, in response to public comment, the agency acknowledged that it is "[t]he practice in the Alaska region . . . to have NMFS, rather than Council staff, prepare the proposed rule for Council action." 71 Fed. Reg. at 17,362. That practice was followed in this case.
On May 24, 2005, NMFS Regional Administrator sent a letter to the Council's Executive Director informing him that the NMFS had "prepared draft regulations" for Amendment 79, providing him with the amendment, draft rule, and related documents, and requesting that he submit the same back to the NMFS "for Secretarial review." A.R. 97. The proposed rule was in fact submitted back to the NMFS, unaltered, by the Council*fn6 two days later, on May 26, 2005. A.R. 66-02 (Council's formal submission of the draft proposed rule to the Secretary). Shortly thereafter, on June 3, 2005, the Council met and discussed Amendment 79 and the proposed rules that had been submitted for Secretarial review. A.R. 118 (transcript of Council meeting). At that time, the proposed rule had not yet been published in the Federal Register for notice and comment, but, since the Council did not expect to meet before the end of the comment period, Council members agreed that the Council should develop any comments it might want to submit ...