An HGMP is essentially a permit application. The hatchery proponent (WDFW, ODFW, Tribe, private entity, etc) is applying for a permit to harm listed species, or "take authorization" in fed-speak. Under the existing 4d Rule, there are 13 areas of activity where agencies or other entities can apply for take authorization. Hatchery production is one of the areas. The rest include harvest, forestry, development, road building, etc.
The 4d Rule recognizes that lots of things are killing or hurting listed salmon and steelhead, but many of them are fairly necessary to modern life. So it's looking for ways to allow those activiteis where possible, but regulate and possibly improve them.
Under the ESA, any activity that harms listed species is technically illegal. Applying for take authorization is like getting a variance. If your permit-application qualifies, you get the variance, probably with some conditioins attached, and you're allowed to carry on whatever activity you applied for. If you don't apply, or don't get the variance, then you're techincally in violation of the law for harming species, and you can be punished and/or sued. What you have to remember is that it isn't necessarily illegal to harm listed species; it's illegal to harm listed species without permission. You can't be sued or punished for not filing an HGMP, but you can be sued for harming listed fish without an HGMP.
In the case of an HGMP, you get the permission by describing the particular hatchery program, including all the benefits to fishing, treaty rights, etc, and all the costs, economic and ecological. If the costs are high relative to the benefits, you describe measures you'll take to try and improve the performance. NOAA then weighs the package and if warranted, grants the take authorization; the public gets to offer input.
Getting an HGMP approved wouldn't necessarily mean that the program didn't hurt wild fish. I might mean that it didn't hurt very much, or that the benefits were worth it, or that the proposed plan to reduce the harm appeared credible. If hatcheries didn't hurt listed fish at all, they wouldn't need HGMPs.
Nobody can make you get the variance, but if then you're activity harms a listed fish, you'll be in trouble, or at least exposed to trouble. You're exposed to trouble as soon as the 4d Rule takes effect, so to be perfectly safe, you'd want to be permited up by then. Of course there are other ways to get take authorization for hatcheries without getting an HGMP (NOAA claims its the most convenient way). Or a hatchery could claim/hope it isn't harming any listed fish and take its chances.
I think NOAA has approved about a dozen HGMPs out of literally hundreds of hatchery programs that need them. The newest existing 4d Rules are like four years old. So technically all those hundreds of hatcheries have been out of compliance with the ESA for four years, not for failing to file HGMPs, but for harming listed fish without a permit. NOAA could fine them, or maybe even force them to close, or they could be sued by virtually any citizen or organization.
So far just about none of that has happened, so the answer to your question about how long agencies can go without filing seems to be anyone's guess. Washington Trout did sue WDFW for unauthorized take of PS chinook from WDFW hatchery operations when the HGMPs were two years overdue. We settled that case for a committment from WDFW to submit all its HGMPs by a specific deadline, and an expanded pubic-input opportunity. WT also recieved $50,000 to recover its litigation expenses, including legal fees. Since the settlement, all PS HGMPs have been submitted; half fo the Columbia River HGMPs are available for public comment now and will be submitted before the end of the year, and the other half will be submitted within a year after that. Not exactly lightning fast action, but better than what we had before, which was no action. To its credit, WDFW made the first Columbia River package of HGMPs available for public comment two months ahead of its deadline.
(None of the HGMPs have yet been approved by NOAA, so most WDFW hatcheries continue to operate without an ESA permit.)
Ramon Vanden Brulle
Washington Trout