The regional head of the Federal Emergency Management Agency (FEMA) resigned today after refusing to alter a draft report questioning the agency's ability to certify the safe evacuation of the Shoreham nuclear power plant on Long Island.

Frank P. Petrone, appointed by President Reagan four years ago, said FEMA director Julius W. Becton told him to resign his $67,000-a-year post or be fired unless he eliminated a sentence in his report on a February emergency evacuation drill at the $4.5 billion plant.

Petrone said Becton was "pressured" by Nuclear Regulatory Commission officials, unnamed "administration officials" and the utility industry to produce a report favorable to the licensing of the controversial plant.

Becton declined to be interviewed. In a statement tonight, FEMA said the sentence expressing Petrone's position "does not comport with the position FEMA has maintained since the NRC [Nuclear Regulatory Agency] directed that a limited exercise of the Shoreham plan be conducted."

A FEMA spokeswoman said the agency was directed by Congressional appropriations subcommittees in November to provide "requisite resources" to develop evacuation plans in the event of "inadequate participation" by state and local officials.

Petrone's resignation highlights a festering dispute within the administration, and within the Republican Party, over the controversial plant.

Gov. Mario M. Cuomo (D) and Suffolk county officials have refused to participate in emergency evacuation planning, on grounds that the area, surrounded by water on three sides, could not be safely evacuated. The federal Atomic Safety and Licensing Board and its appeals panel ruled last year that the utility had no authority to implement an evacuation plan without state and local cooperation.

However, the NRC, which oversees the board, ordered the drill to proceed. In his report on the drill, held in February, Petrone wrote, "Since the [utility's] plan cannot be implemented without state and local participation, FEMA cannot give reasonable assurance under its regulations that the public health and safety can be protected."

FEMA's statement today said the agency told the NRC and the Congress, when the drill was ordered, that without state and local participation, it would "make no finding as to the adequacy" of the evacuation plan. "For FEMA to say it cannot give assurances, as Mr. Petrone insists, is to make a finding."

FEMA spokeswoman Peg Maloy said, "No pressure has been placed on us by the White House or by the NRC."

Sen. Alfonse M. D'Amato (R-N.Y.), who originally recommended Petrone for the patronage job, said he was "shocked and dismayed that FEMA would seek Petron's resignation. This is outrageous . . . . Frank Petrone is telling his Washington superiors that without public input and local government participation, the February Shoreham drill cannot assure the public safety.

"FEMA is, like ancient Greece, killing the messenger because they don't like the message," D'Amato said.

Cuomo called for "a full Congressional investigation," saying, "I applaud the courage and the integrity of Frank Petrone, who resigned rather that bow to pressure from Washington to change his assessment of the safety issues."

Requirements for state and local participation in emergency evacuation were enacted by Congress after the Three Mile Island accident that severely damaged a nuclear reactor near Middleton, Pa.

"The responsiblity given to FEMA after the accident at Three Mile Island is a responsibility I take very seriously: that is to provide an unbiased and impartial review of emergency preparedness to protect people living near nuclear power plants," Petrone said in his resignation letter. "I believe that the credibility of the agency is endangered when national office officials move to overturn critical regional decisions," he said.

Without FEMA's tacit approval, it would be difficult for the NRC to license the plant. But Petrone and NRC officials said today that FEMA told the NRC last fall it would not be able to assure public safety after the drill.

A letter from FEMA official Samuel W. Speck to the NRC Oct. 29, 1985, said, "Any exercise without participation by state and local governments would not allow us sufficient demonstration to reach a finding of reasonable assurance."

NRC commissioner James Asselstine, one of two Shoreham opponents on the five-member commission, said tonight he had "no evidence" of NRC pressure on Becton.

The Petrone resignation comes in the wake of earlier controversy at FEMA. Becton's predecessor, Louis O. Giuffrida, was forced out last fall after misconduct charges.