Energy Secretary James B. Edwards urged the House yesterday to enact legislation creating a permanent underground disposal site for high-level radioactive waste from atomic power plants, but to leave aside disposal of the far larger quantity of waste generated by the U.S. nuclear weapons program.

"I think we should separate the commercial and defense waste programs," Edwards said in testifying before the House energy conservation and power subcommittee.

But while the administration wants to confine the legislation to storage of waste from the civilian nuclear program, a subcommittee source said the bill now in contemplation--which committee leaders hope to have on the House floor by June 30--would not exclude the military.

Thus the treatment of military waste has emerged again as the major issue frustrating legislation to provide permanent nuclear waste disposal, in turn one of the major problems confronting the nuclear power industry.

Both the House and Senate passed waste disposal bills in 1980, but these died when the two houses disagreed over whether states could block storage of military waste within their borders.

Thanks in part to the Reagan administration, the Senate this April passed another bill, and two different versions of nuclear waste bills have been passed by two other House committees.

But the Senate bill provides for disposal of military waste in the same repository as waste from civilian power plants unless the president determines that national security requires separate storage.

Inclusion of military waste in the legislation has been adamantly opposed by both the Senate and House Armed Services committees.

Congressional observers feel that, unless the House Energy Committee reports out a bill that treats the military waste issue in a manner acceptable to the House Armed Services unit, legislation in this session is unlikely.

The military's primary stated objection to comingling defense waste with burned-up fuel from power plants has been that secrets of weapons production might be disclosed as a result of the procedures that will be established to supervise a permanent nuclear waste repository.

Yesterday, however, the Department of Energy indicated a secondary concern: the process for establishment of a permanent site may become so time-consuming that the military might prefer to seek separate legislation enabling it to construct a repository of its own.

The Senate bill requires that the secretary of energy select the first permanent nuclear waste disposal site by 1986 and a second site by 1992.

The current Energy Department timetable calls for opening the first repository, if legislation is enacted, in the mid-1990s.

Radioactive waste from U.S. weapons production already occupies more than 10 million cubic feet in storage tanks at several government sites, far outstripping the waste that has accumulated at the 75 nuclear power plants operating across the nation.

But to charges by Rep. Edward J. Markey (D-Mass.) that the administration's desire to exclude military waste from the legislation meant that the larger part of the nuclear waste disposal problem would be left unsolved, Edwards responded that, while spent fuel from power plants might only amount to 2 percent of the country's total waste by volume, it contained 89 percent of the radioactivity.

Officials from several of the states that are leading candidates for permanent storage facilities strongly argued that the military not be exempted from the provisions that will govern the siting and construction of civilian repositories.

"The environmental, engineering, transportation and political considerations surrounding the disposal of these wastes are identical," contended Utah Gov. Scott M. Matheson in written testimony submitted to the subcommittee.

"It is imperative that the state and local concerns be afforded the same attention regardless of the type and origin of waste to be disposed," Matheson said.