A bitterly divided Nuclear Regulatory Commission yesterday backed down on its threat to shut down the Indian Point nuclear reactors near New York City, even though the government says it still lacks "reasonable assurance" that nearby residents could be protected adequately in an emergency.

The NRC voted, 3 to 2, to permit the two large reactors, in Buchanan, N.Y., to continue operating after the Federal Emergency Management Agency reported that "substantial progress" had been made in eliminating "significant deficiencies" in the plants' emergency plans.

NRC Chairman Nunzio Palladino, who led the commission majority, termed it "highly improbable that an accident" leading to a major radiation release would occur at Indian Point, and said that even if one did, "it most likely would be one that would allow 12 or more hours for responsive action." Palladino said while he had "kept in mind the importance of emergency preparedness" he couldn't "ignore the economic costs of a shutdown . . . . "

But James K. Asselstine, the newest NRC member, argued vehemently that "the public interest and our own regulations" require closing the plants until it is shown that "the public health and safety can be protected in the 10-mile emergency planning zone around Indian Point."

"This makes a mockery of our emergency planning regulations," Asselstine charged. He noted it has been "more than two years since the Federal Emergency Management Agency first notified the commission that significant deficiencies in emergency planning and preparedness existed" at the plants.

"It is difficult to believe that the commission's 120-day procedure warning utilities to correct deficiencies has any meaning at all in light of today's action," Asselstine said.

Commissioner Victor Gilinsky, who also voted to close the plants, pointed out that 290,000 people live within 10 miles of Indian Point--making it the most densely populated area around a U.S. nuclear plant. Noting that Indian Point failed two emergency preparedness tests--with no new test planned for 60 days--Gilinsky charged that the NRC majority did not invite FEMA to yesterday's meeting "apparently for fear that FEMA's comments might undermine the rationale" for keeping the plants open.

Commissioners John Ahearne and Thomas Roberts joined Palladino in voting against shutting down the reactors. "This is a razor-thin decision," said Ahearne, who was considered to be the key vote. "I conclude adequate interim compensating actions have been taken or will be taken promptly."

The vote ended for the moment the possibility that the Indian Point reactors might become the first to be closed for failing to meet emergency planning requirements that were put in place after the accident in 1979 at the Three Mile Island nuclear plant in Pennsylvania.

But the most striking aspect of yesterday's meeting was the sharp break by Asselstine with President Reagan's two other appointees, Palladino and Roberts. With Ahearne's term on the commission expiring at the end of the month, observers had expected that a fourth Reagan nominee would provide a solid pro-nuclear majority.

But yesterday's vote is yet another indication that Asselstine may be a more independent force than the White House originally thought, and suggests that Ahearne's successor may become the swing vote. While the White House has yet to nominate a successor, sources view Frederick M. Bernthal, chief legislative assistant to Senate Majority Leader Howard H. Baker Jr. (R-Tenn.), as the leading contender.