With pointed criticisms of the federal approach to regulating the Massachusetts fishing industry, the state Division of Marine Fisheries yesterday stood by its intention to give most of an emergency $13.4 million appropriation directly to Bay State fishermen.

The thrust of the proposal published on the division's Web site late yesterday morning was no surprise and puts the state agency — along with the state's congressional delegation — on a collision course with the federal fishing regulators in the National Oceanic and Atmospheric Administration.

The division said it expected to make final changes Monday and have the spending proposal in NOAA's offices by the end of work Tuesday. NOAA declined substantive comment until the document was complete.

NOAA took control of the money after it cleared Congress and the White House last December.

John Oliver, the nation's ranking fishing regulator, advised the state that the surest way to get the money quickly, secured on an earmark by U.S. Sens. Edward Kennedy and John Kerry, both D-Mass., was to follow federal policy.

In a letter to the state describing federal intentions toward the fishermen who have been laid low by waves of intricate restrictions over how often, when and where they can fish for cod, haddock, flatfish and minor species in the North Atlantic, Oliver asserted NOAA's goal of reducing the number of fishermen.

The state Division of Marine Fisheries, however, has rejected that approach and spent the bulk of its counterproposal explaining choices made between competing ideas for the formulas that decide who gets how much.

A secondary point of conflict is NOAA's insistence on taking a $481,751 administration fee off the top of the appropriation.

"To date," wrote the division, "NOAA has provided no details on proposed use of these funds."

Kennedy and Kerry sharply criticized NOAA for its determination to take part of the emergency appropriation.

The state proposal also does not mince words about the impact of federal fishing policies.

The latest of these directives — known collectively as Framework 42, and in effect since 2006 — effectively reduced days at sea allowed to federal groundfish permit holders and instituted rolling closures of the best fishing grounds at times fish tend to concentrate.

"The current fisheries management system is making it extremely difficult, especially for the small-boat operations working off the Massachusetts coast, to conduct practical, economically-sound fishing operations," wrote division Director Paul Diodati.

His critique echoes that of Gov. Deval Patrick, who presented NOAA with a scientific study and survey of the fishery last fall and sought a disaster declaration and $23 million in economic aid for fishermen losing their capacity to make a living because of federal efforts to protect the targeted species.

The earmark was the senators' effort to substitute congressional initiative for bureaucratic intransigence. The tug of war over the use of the money was the logical consequence of starkly different policies toward the fishermen of Massachusetts.

"Clearly, the state and DMF have the right priority versus NOAA's proposal for the money," said Gloucester Republican state Sen. Bruce Tarr. "We're talking about preserving the industry into the future."

Tarr said he expects the state's proposal to create an impasse with NOAA.

"The bureaucrats want to consolidate the industry," he said, adding that the state and congressional delegation need "to stand firm."

Kennedy and Kerry declined comment until after the proposal becomes final next week.

"We intend to move (the final proposal) through grant review as expeditiously as possible," said Teri Frade, spokeswoman for NOAA in Gloucester, where the agency has its regional office.

Diodati's draft proposal would set aside nearly 94 percent of the appropriation — $12,575,000 of the $13,395,000 — as direct aid to fishermen.

Not all of the direct aid would be in the form of cash subsidies to boat owners. The state would set aside $500,000 to provide health insurance coverage for fishermen and their families and $500,000 for direct aid to hired crew members.

Diodati said the $12,575,000 would be allocated to federally permitted fishermen, state-permitted fishermen and charter fishermen based on percentage of total groundfish landed in the state in 2007.

Nearly 96 percent was landed on boats of federal permit holders. The bulk of these are New Bedford boats. Diodati's formula also dropped a qualifying requirement that a boat must have landed at least 10,000 pounds of fish in the year.

In Gloucester, which now has mostly smaller boats working day and overnight trips, often using multiple permits, the elimination of the landings requirement means more fishermen can qualify for the aid, Tarr said.

The thrust of the approach taken by the state was to match aid with the relative number of days at sea allowed in the permits. Tarr said he believed this was the most equitable approach.

"Fishermen will be funded based on their investment in the right to fish and the opportunity to fish," Tarr said.

Richard Gaines can be reached at rgaines@gloucestertimes.com