Congress has moved to block President Obama’s plan to shift control of the U.S. drone campaign from the CIA to the Defense Department, inserting a secret provision in the massive government spending bill introduced this week that would preserve the spy agency’s role in lethal counterterrorism operations, U.S. officials said.

The measure, included in a classified annex to the $1.1 trillion federal budget plan, would restrict the use of any funding to transfer unmanned aircraft or the authority to carry out drone strikes from the CIA to the Pentagon, officials said.

The provision represents an unusually direct intervention by lawmakers into the way covert operations are run, impeding an administration plan aimed at returning the CIA’s focus to traditional intelligence gathering and possibly bringing more transparency to drone strikes.

The move also reflects some lawmakers’ lingering doubts about the U.S. military’s ability to conduct strikes against al-Qaeda and its regional affiliates without hitting the wrong targets and killing civilians.

Those apprehensions were amplified after a U.S. military strike in Yemen last month killed a dozen people, including as many as six civilians, in an 11-vehicle convoy that tribal leaders said was part of a wedding procession. U.S. officials said that the strike was aimed at a senior al-Qaeda operative but that reviews of the operation have raised concern that it failed to comply with White House guidelines requiring “near certainty” that no civilians would be harmed.

Sen. John McCain (R-Ariz.) read from a Washington Post story on the Senate floor Thursday, slamming the Senate and House Appropriations committee for amending a spending bill so that it would affect policy with regard to drones. (The Associated Press)

On Wednesday, there were reports that another U.S. strike had killed a farmer in Yemen.

The extent of the restrictions contained in the drone provision remained unclear. The measure was included by members of the House and Senate appropriations committees, said officials who spoke on the condition of anonymity because they were not authorized to comment publicly on the legislation. Other senior lawmakers and congressional officials declined to comment on the contents of the classified annex, which details funding for U.S. spy agencies.

Still, senior lawmakers have been vocal in expressing concern about the prospect of the CIA ceding responsibility for drone strikes to the military. Sen. Dianne Feinstein (D-Calif.), the chairman of the Senate Intelligence Committee and a member of the Appropriations Committee, said last year that she had seen the CIA “exercise patience and discretion specifically to prevent collateral damage” and that she “would really have to be convinced that the military would carry it out that well.”

Feinstein declined to comment on the budget measure this week. But a senior aide said that the senator “stands by her earlier statements” and that the Intelligence Committee has “recently reviewed this issue, and Senator Feinstein believes her views are widely shared on the committee.”

Asked about the scope of that review, the aide said the panel “took stock of” the program and “came to a conclusion” but would not elaborate.

Among Feinstein’s colleagues on the Intelligence Committee is Sen. Barbara A. Mikulski (D-Md.), who is chairman of the appropriations panel responsible for the budget bill. A spokesman for that committee declined to comment.

There is no mention of the drone provision in the hundreds of pages of the budget blueprint released to the public. A section outlining $572 billion in Pentagon spending notes that “adjustments to classified programs are addressed in the accompanying classified annex.”

The Houes voted to adopt the $1.1-trillion measure that funds the government through the fiscal year. (The Associated Press)

A person familiar with the omnibus bill confirmed that the annex includes language on the drone program but would say only that the provision is more complicated than merely withholding money to prevent drone operations from being transferred to the Pentagon.

Former U.S. officials familiar with the intelligence appropriations process said that aside from placing restrictions on funding, Congress could create other obstacles — for example, requiring the Pentagon to certify that it has matched the CIA’s capabilities and targeting methodology before it is allowed to proceed.

Spokespeople for the White House, the CIA and the Pentagon declined to comment.

The spending bill sets budgets for agencies across the federal government for the fiscal year that ends Sept. 30. The measure cleared the House late Wednesday. It is expected to be approved by the Senate this week and delivered to President Obama for his signature as soon as Saturday.

The move by Congress carries implications for the course of the U.S. efforts against al-Qaeda at a time when its affiliates in Yemen, Somalia, Iraq and Syria have become more worrisome to American counterterrorism officials than the terrorist organization’s traditional core.

Also at issue is the fundamental mission of the CIA, which during the past decade has morphed into a paramilitary force. Senior officials, including CIA Director John O. Brennan, have warned that the agency’s emphasis on lethal operations deviates from its traditional mission and could impair its ability to focus on gathering intelligence.

The administration first signaled its intent to shift control of drone operations to the Pentagon last year, when Obama announced new guidelines for counterterrorism missions — including a pledge of greater transparency — during a speech at the National Defense University. At the time, administration officials briefing reporters said there would be “a preference for the Department of Defense to engage in the use of force outside war zones.”

The remark was a reference to Pakistan, Yemen and Somalia — countries beyond the war zones of Iraq and Afghanistan, where the United States has carried out drone strikes against al-Qaeda targets.

Obama’s policy shift was expected to mainly affect Yemen, where the CIA and the elite U.S. Joint Special Operations Command conduct overlapping drone campaigns.

The overall pace of strikes has diminished significantly in Pakistan and Yemen, and Brennan has held secret meetings with Pentagon officials in recent months to work out logistical challenges and other impediments to shifting control of drone operations.

But the CIA still carries out the majority of strikes, and the collateral damage that has accompanied some JSOC strikes has generated growing opposition to removing the agency from such operations anytime soon.

The Pentagon has refused to release any details on the Dec. 12 strike carried out by JSOC in Radaa, a district that has become a stronghold for al-Qaeda in the Arabian Peninsula, or AQAP. Yemen initially insisted that only militants had been killed, but it later acknowledged civilian casualties.

The government then delivered rifles and other compensation to victims’ families — payments that a Yemeni official described as a “deposit” to encourage clan leaders to take part in tribal mediation and accept further compensation rather than seek retaliation against the Sanaa government.

“There was a [legitimate] target, and then something happened, a misfire,” the Yemeni official said, speaking on the condition of anonymity because of the secrecy surrounding U.S. strikes. “I’ve never been aware of any incident before where a strike targeted such a large convoy of vehicles.”

AQAP is responsible for near-miss attacks on the United States, including the attempted bombing of a Detroit-bound airliner on Christmas Day in 2009. The terrorist group has been driven out of territory it had gained over the past two years but is still considered by U.S. officials to pose a serious threat to the United States.

In a meeting with U.S., European and Middle Eastern diplomats last week, Yemeni President Abed Rabbo Mansour Hadi described the security situation as unstable and warned specifically of indications that potential al-Qaeda recruits from European and other Western nations were seeking to enter the country, according to U.S. and Yemeni officials.

Lori Montgomery and Ed O’Keefe contributed to this report.