DENVER, JUNE 9 -- The FBI has charged that senior executives in the Energy Department knew for years about illegal and dangerous toxic-waste procedures at the Rocky Flats nuclear weapons plant here but lied about the situation to conceal the violations. As a result, according to an affidavit filed in U.S. District Court by the bureau's top environmental law agent here, the Federal Bureau of Investigation undertook secret ground and aerial surveillance of its fellow federal agency in an investigation code-named "Operation Desert Glow." That spawned this week's raid of the Energy Department plant by 75 federal law enforcement officials. The affidavit charges that Energy Department officials in Washington were aware of the violations. It quotes a 1986 DOE memo warning top officials that some waste practices at Rocky Flats were "patently 'illegal.' " The internal memo said misleading department statements had kept the public from knowing "just how really bad the site is." In Washington, the Energy Department issued a statement today repeating that the investigation had shown no threat to "the health or safety of the public or plant employees" but declined to comment on charges in the affidavit. The department's first comment on the Rocky Flats investigation could come next week, the statement said. Over the last year, the Energy Department has been rocked by repeated charges of mismanagement and dangerous practices at its nuclear fuel and weapons plants nationwide. The current investigation at Rocky Flats, directed by the Justice Department and the Environmental Protection Agency, involves the most detailed allegations of criminal activity by officials at the Energy Department. The problems at Rocky Flats pose tough political decisions for President Bush and Colorado Gov. Roy Romer (D), both of whom have authority to stop work there. If they permit the plant to continue operating, they could face charges of endangering neighborhoods surrounding the site 16 miles north of central Denver. But to shut the nation's only plant making plutonium weapons would cripple supply of the nation's nuclear arsenal and could cost this economically ailing state nearly 6,000 stable, well-paid jobs. Rockwell International Corp., which manages Rocky Flats under federal contract, also has declined to comment specifically on the FBI investigation. Romer said today he was outraged about the toxic dangers set forth in the FBI affidavit and just as angry that the information was kept secret for months by the criminal investigators. FBI special agent Jon Lipsky reported that he flew repeatedly over the Rocky Flats site in an FBI surveillance plane last December. Lipsky said he saw toxic pollutants being released into the atmosphere from an incinerator and a waste-water plant. Romer did not learn of this until today, when the affidavit was unsealed after legal action by the Rocky Mountain News of Denver. "It's absolutely inexcusable," the governor said, "that the information was kept from the people of Colorado . . . . It's more important to protect a person's health than to send somebody to jail." The FBI affidavit was filed to gain a judicial search warrant at the plant. The warrant was issued Tuesday, and the search is expected to continue until next week. In such affidavits, the bureau usually states its case in tough language. In this one, Lipsky discusses Energy Department officials in tones that the FBI might use for mobsters or drug runners. "There is probable cause to believe that Rockwell and DOE officials falsely certified . . . that Rocky Flats was in compliance," the FBI charged. "There is probable cause to believe that DOE and Rockwell have made false statements or concealed material facts . . . {and} criminally violated the Clean Water Act . . . that hazardous wastes have been illegally treated, stored and disposed of and that false statements have been made." The affidavit quotes an internal Energy Department memorandum that was dated July 14, 1986, and concluded that "our permit applications are grossly deficient (some of the waste facilities there are patently 'illegal'). We have serious contamination." But while top officials were receiving such information, the affidavit charges, they told state and federal enforcement agencies that the plant complied with environmental laws. The affidavit criticizes the Energy Department for paying Rockwell a performance bonus even though "DOE officials were aware of severe contamination and were informed that the monitoring system was deficient." In Washington, a lawyer for the Sierra Club, which had raised charges of illegal waste-burning at the plant in a lawsuit, called for an immediate shutdown of Rocky Flats, saying the affidavit contradicts earlier assurances by the Justice and Energy departments that the pollution poses no threat to the public. "The most surprising thing is the blatant lying and illegal activity which was allowed to go along for a considerable period," said the lawyer, A. Blakeman Early. "This doesn't happen by accident. This is active propagation of falsehoods at the highest level." The investigation could seriously hurt Energy Secretary James D. Watkins' effort to fight off legislation that would place his department's nuclear facilities under increased and independent scrutiny, congressional staff aides said. The aides said, however, the allegations are so serious that they could give Watkins, a retired Navy admiral, the motive to, as one put it, "clean house." "Politically, it should be sending shock waves through the Department of Energy," a Senate aide said. Noting that other Energy facilities have been confronted by similar environmental problems, the aide said: " . . . Where else in the Department of Energy has this been happening?"