Environmental Protection Agency official Louis J. Cordia resigned yesterday, hours after it was confirmed that he had compiled a "hit list" of agency employes to be fired, hired or promoted because of their political leanings.

At the same time, senior officials at the agency said Cordia, 28, is a focus of a new internal investigation into charges of mismanagement and alleged tampering with agency records in the Office of Federal Activities, where Cordia had been the No. 2 official until he was demoted Friday.

"Lou has become the focal point of some unfortunate controversy," said Cordia's attorney, former representative Charles E. Wiggins (R-Calif.). "In the interests of the agency and the interests of the administration, he deemed it to be in his best interest to resign."

Acting EPA Administrator John W. Hernandez Jr. accepted Cordia's resignation during an hour-long meeting late yesterday, Wiggins said.

EPA Inspector General Charles L. Dempsey began investigating Cordia, officials said, after a subordinate accused him of ordering the erasure of computerized data requested by The Washington Post under the Freedom of Information Act.

Cordia denied the charge through his attorney. Cordia was stripped of all management responsibilities by Hernandez soon after Dempsey's investigation began.

Also yesterday, Rep. Mike Synar (D-Okla.), chairman of one of six subcommittees investigating the EPA, confirmed that a list was found in Cordia's files designating certain agency employes as "unacceptable to this administration," and others desirable because of their conservative views.

The list, in Cordia's handwriting, was on the stationery of the Heritage Foundation, the conservative think tank where Cordia worked before joining the EPA in late 1981.

In addition, Dempsey's internal probe expanded yesterday, according to several EPA officials, to include charges of mismanagement and employe harassment in the Office of Federal Activities, where Cordia worked.

The office is the watchdog over the environmental and health impacts of all federal government projects--from nuclear power plants to cattle-grazing programs.

Several EPA officials said yesterday that Cordia and Paul Cahill, the office director, politicized the program by rewriting the reports of staff scientists who raised environmental objections to administration projects.

The most recent example, they said, came in January, when Cahill gave the go-ahead for the reopening of the Savannah River Plant, an idled nuclear reactor, despite conclusions by staff scientists that it could pose major health hazards.

"That office illustrates the way government policies can be changed outside the regulatory process," said a senior EPA official critical of Cordia and Cahill. "If you can't change the bureaucracy, ignore it and just bring in your own people."

Cahill did not return telephone calls yesterday.

The lists on the Heritage stationery were sent by Cordia, apparently in July, 1981, to two EPA officials. "Please do not share the recommendations and staff lists with anyone," wrote Cordia. "I would feel the backlash. I also repeat that the comments on both lists are not conclusive evidence but rather serve only as indicators from my advisers."

The lists deal mainly with top political positions and senior career managers. John A. Todhunter, a lobbyist for an industry supported research group who now runs the EPA office of toxic substances and pesticides, was described as a "must" for a top job.

Another official was said to be "supportive of the new administration if the new administration is for nuclear power, business and conservative interests."

Val Adamkus, who became the EPA's Chicago regional administrator, was said to have been recommended by "some oil." The list also said of Adamkus: "Understand to have brought in many votes on 11/4," Election Day.

Senior EPA officials said they are investigating whether Cordia and Cahill interfered with an inquiry under the Freedom of Information Act. Cahill answered the request by mailing a report showing that his office had completed 90 percent of the environmental reviews required by federal laws. However, several sources said, EPA documents showed the office has completed only 25 percent of the reviews.

Cahill's response omitted those documents and did not mention a computer printout that the sources said had been prepared, showing 19 staff reviews of federal projects have not been filed by Cahill or Cordia.

Wiggins, Cordia's attorney, said his client had not inflated the number of reviews completed by the office and had not blocked the release of any reviews. "Everything has gone out routinely," he said.

Cordia said through Wiggins that the employe who accused him of ordering erasures had "misunderstood" his instructions. He said he believed the computerized information "had to be supplemented, not erased."

EPA officials said 24 of the 47 career employes in the office have left since Cordia and Cahill arrived in October, 1981. They said many scientists and Ph.Ds in the office had been reassigned to clerical jobs such as the cutting and pasting of organization charts and hole-punching in documents that needed to be bound.