The United States and Afghanistan signed an agreement Sunday putting Afghans in charge of special operations, including controversial night raids on Afghan homes that have been a major source of contention between the two sides.

Afghan Defense Minister Abdul Rahim Wardak and the U.S. commander of NATO forces in Afghanistan, General John Allen, signed the deal at a ceremony in Kabul.

The agreement appears to give Afghan authorities veto power over planned operations. It sets up an Afghan Operational Coordination Group that will approve special operations, which will be conducted by Afghan forces with support from U.S. forces “in accordance with Afghan laws.” It also states that U.S. forces will join Afghan security forces entering private residences “only as required or requested.”

The agreement also gives Afghan authorities more say in the treatment of detainees.

Wardak said Sunday that special operations will now be “Afghan-owned” and conducted by a special contingent of forces from the defense and interior ministries, and the national security directorate.

General Allen said the agreement marks a “significant milestone” in advancing Afghan sovereignty and in shared efforts to formalize a long-term U.S.-Afghan strategic partnership.

The U.S. ambassador to Afghanistan, Ryan Crocker, called the agreement “an important illustration of our commitment to Afghan sovereignty and of our strong partnership as we move forward to completing the transition of responsibility for Afghanistan's security to Afghan forces by the end of 2014.”

Afghan President Hamid Karzai had called repeatedly for an end to all international night raids, saying they are provocative when carried out by foreign forces. But NATO commanders have said the operations have proven extremely effective in apprehending Taliban insurgents and al-Qaida commanders.

There is growing sensitivity in Afghanistan over the presence of foreign troops after a series of incidents, including the killing of 17 Afghan villagers – for which a U.S. soldier was charged – and the inadvertent burning of copies of the Quran at a NATO base.

U.S. officials hope Kabul and Washington will be able to reach a strategic partnership agreement in time for next month's NATO summit in Chicago. The deal will govern relations between the two countries after the scheduled 2014 pullout of foreign forces from Afghanistan.