The administrator of the Environmental Protection Agency today approved the controversial cooling system for the massively protested proposed $2 billion nuclear power plant here.

That ruling, issued in a 49-page statement by EPA Administrator Douglas Costle in Washington, overturned the former New England regional EPA Administrator's determination that the plant's cooling system did not meet requirements of the Federal Water Protection Act.

The former regional administrator. John McGlennon, and various enviromental groups, had objected to the proposed system's discharge each day of more than 1 billion gallons of water about 39 degrees hotter than the ocean.

In issuing his ruling, which he emphasized was a narrow, technical one. Costle placed tight enviromental restrictions on the 230 megawatt plant, but noted. "The information in the record was sufficient to determine that ocean life would be adequately protected."

The ruling calls for protection of marine life in the coastal estuary from the heated water. It requires the power company to extend a 19-foot-in-diameter intake water pipe from 3,000 to 7,000 feet into the ocean to suck in water from less densely populated sea life areas.

Officials of the privately owned Public Service Co. of New Hampshire, builders of the controversial plant, claim that additional pipe will cost about $12 million.

The Environmental Protection Agency's decision still leaves at least one more obstacle before construction can continue.

The power company must still receive approval of its design from the Nuclear Regulatory Commission before the projected 3,000 workers can resume operations at Seabrook.

But power company officials are optimistic that the suspension will be lifted within the next several weeks since the NRC in 1976 issued a construction permit before bowing to the EPA objections. This will finally clear the way for construction after seven years of environmental studies, and five years of hearings and court battles.

Public Service Co. spokesman Donald Lundholm waved off the objections of groups like the Sea Coast Anti-Pollution League and the Clamshell Alliance, a group which staged an anti-nuclear power protest on the Seabrook construction site on the weekend of May 1, in which 1,414 were arrested.

"The environment won't be harmed to any reasonable degree if the system operates as proposed," he said.

The Clamshell Alliance held a 12-hour vigil in Boston's Government center and on the Boston Commons today in support of the former regional EPA administrator's decision against the cooling system. The antinuclear group was expected to hold a demonstration in front of the construction site here Saturday.

Two oceanographers hired by EPA to perform independent evaluation of the scientific data gathered concerning Seabrook's impact criticized the decision.

"From the data given . . . nobody can say there wouldn't be any harm to the environment," said Edward Carpenter, a professor of oceanography at the State University of New York at Stoneybrook. "You also can't say that there would be damaged. The data simply isn't conclusive."

"EPA presented us with a number of questions," said Dr. Theodore Smayda, oceanography professor at the University of Rhode Island. "The central issue was whether or not the effects of the discharge could be reasonably predicted from the data. My answer was 'No.'"

Meanwhile, local nuclear power and "pro-job" groups also have planned a rally in Manchester, N.H., on June 26.

Frank Katowski, the utility company's Seabrook information representative, claimed delays in approving the project have added about $15 million a month for the past six months to the project's cost because of bond interest payments, inflation and labor and material costs and rescheduling of material deliveries.