Afghan President Hamid Karzai on Monday hailed an agreement with the United States over controversial night raids by special forces as consolidating Afghan sovereignty.

Night raids by international troops targeting insurgents in their homes have been a stumbling block in efforts by both countries to reach a treaty covering relations after most US-led foreign troops pull out by the end of 2014.

The deal signed Sunday puts Afghans in charge of the night operations, deemed a key tactic in the fight against Taliban insurgents by the US but condemned locally as as a breach of the sanctity of Afghan family homes.

"In accordance with this agreement we assure people that not only the foreigners will not enter people's houses, but also the Afghan government will not harm anyone and that human rights will not be violated," Karzai said.

All government agencies should prove that the government was the protector of the interests, security and lives of Afghans "so that people after years of suffering finally feel safe in their homes," Karzai said.

"Afghan sovereignty was consolidated (by the agreement) and the Afghan government has taken the lead," he told a cabinet meeting, according to a statement from the presidential palace.

Sounding a note of caution, First Vice-President Marshal Fahim added that the government "emphatically asks people not to allow terrorists in their houses", the statement said.

Western military commanders have stressed that night raids are important in the bloody war against Taliban insurgents, who have been fighting Karzai and his international allies for more than a decade.

The deal, covering all special operations in Afghanistan, is expected to pave the way for a strategic partnership pact between Washington and Kabul on the US presence after most of the 130,000 US-led NATO troops leave.

US military officers envisage a follow-on force of around 15,000 personnel in Afghanistan, focusing on air power, logistics, training, intelligence and counterterrorism.