The recently approved 1991 defense spending bill tightens Congress's controls over the Pentagon's classified, or "black", programs following incidents in which defense or intelligence agencies "ignored or challenged" directives of the legislative branch on how the money should be spent.

The existence of friction involving the multibillion-dollar classified budget was acknowledged in a letter made public yesterday by the office of Senate Appropriations Committee Chairman Robert C. Byrd (D-W.Va.).

"The decisions reached after long deliberation by our committee on these programs are sometimes at variance with the desires of the executive branch, sometimes controversial, and have in a number of recent important situations become matters of dispute between the two branches," Byrd wrote last month to Rep. John P. Murtha (D-Pa.), chairman of the House Appropriations defense subcommittee.

Consequently, a new provision was added to the defense bill that gives the force of law to the classified report accompanying the measure. "There's no question about it, it's the law," said Murtha in an interview yesterday.

Congressional sources declined to identify the programs that have generated the tensions, but outside specialists suggested that the dispute results from financial constraints and growing uncertainties about the future mission of the military and intelligence communities.

"The reason you're having these procedural problems is that you have a fundamental debate about what the intelligence community ought to be doing," said John Pike of the Federation of American Scientists.

At the same time, as the Cold War appears to wane, the Pentagon's secret weapons programs are coming in for the same kind of reappraisal as the overall Pentagon budget. Among programs that remain highly classified are the Navy's antisubmarine warfare research and the Air Force's air-to-air missile of the future.

This debate is sharpened by hefty cuts this year in the Pentagon budget, which is used to conceal funding for classified intelligence and military programs. Huge sums of money are involved. The Defense Budget Project calculated that President Bush's proposed 1991 budget for classified procurement and research came to some $28 billion. Other estimates range up to $36 billion.

Some of the most expensive weapons in the Pentagon's arsenal, including the B-2 "stealth" bomber, the Advanced Cruise Missile and the Advanced Tactical Fighter began as classified programs largely shielded from public debate.

"We've changed dramatically what's happening in black programs," said Murtha, who ordered a review of the classified budget last year when he became chairman of the Appropriations subcommittee. He said classified programs were cut more than the Pentagon budget this year as a result of identifying programs that were not being run efficiently or were no longer necessary.

"They were not scrutinized as carefully as they should have been," he said.

One example of tensions between Congress and the administration over an intelligence program involved the SR-71 high-flying reconnaissance plane. Sources said the National Reconnaissance Office, which operates U.S. spy satellites, favored ending the program. But some in Congress wanted to keep it for cost-saving reasons. The appropriators shut down the program last year.

The appropriators have faced a special problem in forcing the administration to follow its guidelines for classified spending. Appropriations bills end up as public laws which, by definition, are unclassified. Therefore, directives to the executive branch have had to be put into an annual classified annex. The administration has argued that this constitutes only advice and does not have legal force.

But the new defense measure Congress has asked Bush to sign into law contains a provision stating that the classified annex has the force of law.

Byrd told Murtha that there were "fundamental constitutional and institutional questions at stake . . . . Will the checks and balances as they now are in place between the two branches have equal relevance and force in relation to the highly classified agencies, budgets and programs that have grown in the last several decades?"