After months of negotiations, the U.S. and Afghanistan reached an agreement on Sunday that will transfer more control of controversial night raid operations to Afghan forces, allowing the two governments to move ahead in negotiating a broader strategic-partnership agreement.

Night raids — the signature tactic of the U.S.-led kill/capture campaign during which U.S. special forces, accompanied by Afghan troops, search private residences for suspected insurgents — have long strained relations between the two countries. Though the U.S. military touts the operations as the most effective means of putting pressure on the Taliban with the fewest civilian casualties, Afghan President Hamid Karzai has repeatedly called for their end, describing the raids as an affront on the sanctity of Afghan homes and warning that they further fuel the insurgency.

The new agreement requires that a warrant be issued by an Afghan court within 72 hours of a raid taking place, and that Afghan forces lead the raids. Afghan commanders can still request U.S. support and intelligence at any time for an operation.

A major sticking point in the negotiations was determining who would have authority over those detained in the raids.  The two sides agreed that Afghan forces will hold detainees and decide whether U.S. interrogators can have access to them — a significant change from the present scenario in which the U.S. can interrogate and hold detainees indefinitely without trial. However, western officials told The New York Times they were not worried that the Afghans would restrict their access.

There are several notable exceptions in the agreement: The deal does not apply to the small number of night raids carried out by the CIA and “other auspices,” according to The Times. In cases where intelligence must be acted on immediately,  a warrant can be issued after the raid. And though Afghan forces will lead the raids, vague language in the agreement allows U.S. forces to join a raid “as required or requested.”

The deal has raised some questions: Newsweek‘s Ron Moreau and Sami Yousafzai wrote that it “seems to put a rather cumbersome bureaucracy in command of operations that need to be lightening fast as the targets of the raids move constantly.” They say that even Taliban commanders have attested to the nighttime operations’ effectiveness, with one one senior Taliban commander in eastern Afghanistan telling them, “We have lost the highest number of ground commanders in these night raids.”

The new policy may also raise human rights concerns about the treatment of detainees in Afghan prisons, which have been accused of systemic human rights abuses in the past.

Perhaps most of all, the deal highlights that despite concerns on both sides, Afghans will have to grapple with the costs.

“Villagers can’t stop the Taliban from entering their houses nor can they stop the night raids,”  a senior Afghan police officer in Ghazni province told Newsweek. “So once again the Afghan public is sandwiched between the U.S. and the Taliban.”