The 222-199 vote sent the measure to the Senate, which still must act before it can go to President Bush. The White House has threatened a veto.
The bill, a House-Senate compromise to authorize intelligence operations in 2008, also blocks spending 70 percent of the intelligence budget until the House and Senate intelligence committees are briefed on Israel's Sept. 6 air strike on an alleged nuclear site in Syria.
The 2008 intelligence budget is classified, but it is more than the $43 billion approved for 2007.
Most of the bill itself also is classified, although some portions were made public. One provision requires reporting to the committees on whether intelligence agency employees are complying with protections for detainees from cruel, inhumane and degrading treatment. Another requires a report on the use of private contractors in intelligence work.
It is the first intelligence authorization conference bill Congress has produced in three years.
The White House threatened to veto the measure this week in a lengthy statement, highlighting more than 11 areas of disagreement with the bill.
The administration particularly opposes restricting the CIA to interrogation methods approved by the U.S. military in 2006. That document prohibits forcing detainees to be naked, perform sexual acts, or pose in a sexual manner; placing hoods or sacks over detainees' heads or duct tape over their eyes; beating, shocking, or burning detainees; threatening them with military dogs; exposing them to extreme heat or cold; conducting mock executions; depriving them of food, water, or medical care; and waterboarding.
Waterboarding is a particularly harsh form of interrogation that involves strapping down a prisoner, covering his mouth with plastic or cloth and pouring water over his face. The prisoner quickly begins to inhale water, causing the sensation of drowning.
The CIA is known to have waterboarded three prisoners but has not used the technique since 2003, according to a government official familiar with the program who spoke on condition of anonymity because the information is classified. CIA Director Michael Hayden prohibited waterboarding in 2006. The U.S. military outlawed it the same year.
The intelligence authorization bill also creates a new internal watchdog to oversee all the intelligence agencies. It requires Senate approval for the first time of two agency heads the National Reconnaissance Office, which manages the nation's spy satellites, and the National Security Agency, the outfit that conducted warrantless wiretapping on American phone and computer lines in what the White House calls the Terrorist Surveillance Program.
Separately on Thursday, the Senate Judiciary Committee rejected legislation that would have protected telecommunications companies from civil lawsuits over helping the government eavesdrop on Americans' communications without court orders. The legislation would have made the government the defendant in such lawsuits, rather than telecommunications companies. The 5-13 vote sank the measure pushed by Sen. Arlen Specter, a Republican who hoped it could be a compromise in the dispute over whether to immunize the companies from lawsuits.
In competing legislation written in October, the Senate Intelligence Committee granted legal immunity to telecom companies. The House passed a bill that does not protect the companies. The White House has also threatened to veto that bill.
Director of National Intelligence Mike McConnell was briefing the Senate in a closed session about the matter on Thursday.