KABUL, Afghanistan — Negotiations over a long-term U.S. military presence in Afghanistan have bogged down over issues of detainees, night raids and quarrels within the Afghan president’s inner circle, throwing the whole deal into question.
The arrangement would formalize a U.S. role after NATO’s planned pullout in 2014. The deadlock reflects growing hostility on the part of the Afghan leadership and increasing exasperation in Washington.

Trust has eroded in recent days with anti-American protests over Quran burnings at a U.S. base, a rising number of U.S. troops gunned down by Afghan security forces and election-year demands to bring the troops home.

Karzai met Monday evening with U.S. Ambassador Ryan Crocker, but a Karzai spokesman did not return phone calls requesting details about their talks. Karzai has scheduled a news conference on Tuesday; it is unclear whether he will discuss the negotiations.

U.S. Embassy spokesman Gavin Sundwall would not disclose any information about the meeting.

Earlier, Sundwall said that despite the dragging negotiations, the U.S. was committed to a strategic partnership with the Afghan people. However, he also said it was more important to get the right agreement than to get an agreement.

The pact is expected to provide for several thousand U.S. troops to stay and train Afghan forces and help with counterterrorism operations. It aims to outline the legal status of those forces, their operating rules and where they will be based. The agreement, which was supposed to be completed before the next NATO summit in May in Chicago, also is seen as means of assuring the Afghan people that the U.S. does not plan to abandon the country, even as it withdraws its combat forces.

NATO’s nighttime raids targeting insurgents are an especially touchy matter.

As part of the agreement, Karzai has said that Afghans should be the only ones conducting the night raids, because the invasion of privacy from troops entering a family’s home is compounded when the soldiers are Westerners. He has also complained that too many raids have resulted in the detention of non-insurgents or civilian deaths. NATO argues that no shots are fired in more than 85 percent of the raids.

An even thornier issue is detentions. Karzai is demanding that the United States transfer control of its main prison in the country — the Parwan Detention Facility, which adjoins Bagram Air Field in eastern Afghanistan — to Afghan control. Karzai thinks having the United States running prisons in his country is an affront to Afghan sovereignty. First he demanded that the prison be handed over by early February, then extended the deadline to this Friday.

The Obama administration has said that the Afghan judicial system is not yet capable of taking over responsibility for dangerous battlefield detainees. The U.S. is willing to work with the Karzai government to complete a transition of detention operations “in a manner that is safe and orderly and in accordance with our international legal obligations,” Sundwall said.

Afghan officials say privately that a U.S. proposal to hand over the facility in six months would be acceptable to some members of the Karzai government, but the president had not embraced the idea.

Karzai tried to bolster his argument by citing the incident on Feb. 20, when Qurans and other Islamic texts from a library at the Parwan Detention Facility were burned. He said that if Afghans had been running the prison, Muslim holy books would never had been sent to a garbage burn pit.

The incident, which Afghans viewed as evidence that foreign forces disregard their culture and Islamic faith, prompted six days of anti-American protests across the nation. During the demonstrations, 30 people died, including six U.S. troops who were killed when Afghan security forces turned their guns on the Americans.

On Monday, the Taliban took responsibility for a suicide bombing outside Bagram that killed two people, saying it was revenge for the Quran burnings.

In other violence Monday, the Interior Ministry said one civilian was killed and 11 people wounded when a man blew himself up at a police checkpoint in Jalalabad in the east.

Karzai has been stubborn about his demands — apparently so much so that he is losing the backing of some of his own top aides.

An Afghan government official, speaking on condition of anonymity to discuss the sensitive negotiations, said that more than two months ago National Security Adviser Rangin Dadfar Spanta submitted his resignation after disagreements erupted between him and Karzai over the strategic partnership document.

Spanta, who is heading the talks, wants Karzai to compromise on night raids and detentions.

Karzai did not accept Spanta’s resignation, but kept the letter.

Spanta was on a trip to China and not available to comment, but Moradian said the resignation threat was part of an effort to pressure Karzai into a compromise.

“There is a possibility that if that tactic didn’t work he would resign,” said Moradian, assistant professor of political science at American University in Kabul.

Moradian, who was the chief policy adviser to Spanta when he was foreign minister, said he thinks Washington is considering waiting to negotiate the deal with Karzai’s successor. Karzai is set to leave office after his second term ends in 2014.