The Environmental Protection Agency has issued about 240 formal operating permits to hazardous-waste disposal facilities, which leaves about 5,000 to go, according to a list released this week by two public-interest organizations.

The list, obtained through Freedom of Information Act requests by the Environmental Safety group and distributed by Public Citizen, shows that most of the sites that have gone through the full-scale licensing procedure are owned by the military or by industrial facilities that use them to handle on-site toxic waste.

Relatively few are sites owned and operated by private waste-management firms of the sort that the agency uses to dispose of waste from sites cleaned up under the federal "Superfund" law.

Disclosure of the list is another case of bad timing for the EPA, which has had a rough time lately explaining why Superfund waste is ending up in landfills that appear to be leaking and could eventually pose as much of a health threat as the original cleanup sites.

Environmental groups and congressional committees have long complained that the agency isn't moving fast enough to investigate hazardous-waste disposal sites, weed out the bad apples and license the rest under the strict provisions of the Resource Conservation and Recovery Act (RCRA).

Until that job is done, EPA officials have acknowledged, the agency won't really know whether the nation's toxic waste is being handled properly.

The situation hasn't exactly pleased the waste industry, either. An official of the Institute of Chemical Waste Management noted in a recent speech that last year, eight years after the enactment of RCRA, the EPA granted permits to only 12 incinerators and six landfills. The agency didn't grant any permits last year for treatment facilities, apparently because it hasn't developed any standards by which to judge their performance.

In recognition of the problem, assistant administrator Lee M. Thomas recently established a national permit strategy that gives first priority to applications from landfills and incinerator facilities.

According to Superfund office spokesman Russ Dawson, sites receiving waste from Superfund cleanups will go to the head of the line for licenses.

"I don't know what the strategy was up until now," he said, "but this is what it is now."

The new strategy has its detractors as well. The waste industry complains that it is directed at closing down bad facilities instead of promoting new facilities and new waste-treatment technologies. DISAGREEMENT IN THE RANKS . . .

A longtime internal critic of EPA's policies has taken EPA Administrator William D. Ruckelshaus to task for suggesting that the agency was largely unaware of the hazardous-waste problem until Love Canal emerged as a national disaster in the late 1970s.

In an article in this month's issue of the EPA Journal, an agency publication, Ruckelshaus wrote that "10 years ago, for all practical purposes, we were unaware that there was a hazardous waste problem." Solid-waste experts didn't become aware of the problem until "the revelations of the late seventies," he wrote, "when the careless disposal practices of the past began to turn places like Love Canal and the Valley of the Drums into images of environmental calamity."

Ruckelshaus has made the same assertions in recent speeches, generally in the context of cautioning his audience not to expect too much too soon from an agency facing such a monumental task.

But in a letter to the EPA Journal, William Sanjour, a solid-waste analyst who also was at the EPA in its early days, said Ruckelshaus "does not seem to be aware of the very significant hazardous waste management program in EPA in the 1970s."

Eleven years ago, the EPA gave Congress a 110-page report on hazardous-waste disposal, he wrote, adding: "There is very little said in your October issue . . . that you would not find in that report."

Moreover, he said, EPA spent "tens of millions of dollars" gathering information on hazardous waste in the early '70s, and by 1975 had "collected a dossier on over 400 hazardous waste disaster sites," most of which are now on the Superfund cleanup list.

Sanjour wrote, "It is a pity that a decade of good work by some very dedicated people at EPA is being written out of history."