KABUL, Afghanistan — Secretary of State John Kerry and Afghan President Hamid Karzai smoothed over one of the worst patches in the difficult relationship between the United States and Afghanistan with smiles and a compromise Monday that settles — for now — a bitter dispute over the fate of Taliban prisoners deemed a threat to U.S. forces.

The transfer of the Parwan detention center is symbolic of the larger tension as U.S. forces depart from Afghanistan after 13 years, leaving behind a fragile democracy with untested ability to defend itself or safeguard the political and economic gains underwritten by billions in U.S. spending.

With a self-imposed deadline of December 2014 for American combat forces to leave Afghanistan, the Obama administration is trying to shape a less volatile relationship with Karzai while insisting on a clean election next year to replace him. Kerry put his long friendship with Karzai on full display Monday, praising him for courage and endurance while Karzai repeatedly thanked Kerry and other American officials for sticking by him.

“You, I think, stand on the brink of a remarkable legacy for having brought Afghanistan through an amazingly difficult time,” Kerry told Karzai. “There are still difficulties ahead; there are still challenges.”

Kerry knows the unpredictable Afghan leader well and was a frequent intermediary for President Barack Obama while serving in the Senate before becoming secretary of state last month.

The two nations are trying to sort out difficult issues that often pit U.S. goals for the security of U.S. forces and American interests against Karzai’s keen sense of national sovereignty.

The largest of these issues remains open: whether any U.S. forces that remain in the country for training and counterterrorism operations after 2014 would be immune from prosecution under Afghan law. U.S. officials say that protection is essential for a long-term joint security agreement, but it will be a hard sell to Afghans. The same dispute sank a hoped-for security agreement that would have left a training and stability force in Iraq.

U.S. officials say it would be foolish to think the process of separating U.S. and Afghan control will be smooth, and some of Karzai’s recent statements are Exhibit A.

New Defense Secretary Chuck Hagel canceled a news conference with Karzai earlier this month after Karzai was widely quoted accusing the Obama administration of colluding with the Taliban insurgency that has tried to overthrow him for a decade. The remark angered U.S. officials and many in Congress.

Kerry and others have assured Karzai that direct talks between the United States and the Taliban remain on hold, and Karzai claimed Monday that his complaint had been misunderstood.

Karzai attempted to put into context some of his recent inflammatory remarks, particularly his accusation that U.S. troops had tortured civilians outside Kabul.

“When I say something to this effect, it’s not to offend our allies but to correct the offense,” Karzai said. “I am the president of this country. It’s my job to provide all the protection I can” for Afghans.

Kerry seemed ready to let the matter slide.

“I am confident that the president absolutely does not believe the United States has any interest except to see the Taliban come to the table to make peace,” while helping Afghanistan defend itself, Kerry said following lengthy meetings at Karzai’s graceful stone palace.

Relations between Karzai and the White House have been fraught for years, with periods of close cooperation alternating with periods of U.S. frustration and Afghan anger.

Karzai’s rhetoric was noticeably more muted at the press conference with Kerry, where he focused largely on his appreciation of the U.S. contribution in Afghanistan. With the handover of the Parwan detention center and the U.S. announcement last week that troops would be gradually removed from Wardak province, it appears that Karzai’s most vehement demands have had an impact.

Kerry and Karzai praised a prison agreement both men said ensures that Afghan sovereignty over its own affairs is respected. Details of the deal were scant, such as whether the United States would maintain veto power over the release of 30 to 40 “enduring security threats,” who American officials say still pose a serious danger to U.S. and Afghan troops.

“It is important for the people of Afghanistan,” Karzai said of the prison, which has been a symbol of sometimes heavy-handed U.S. military control. “It is very closely linked to our sovereignty, and our sovereignty has to be respected.”

Kerry said Karzai “agrees that there are certain people there who shouldn’t be out creating problems,” and Karzai described a process for reviewing any cases on which the United States and Afghanistan disagree. He was vague about what would happen if that review failed to resolve the differences.

It is also unclear whether the U.S. mechanism of “administrative detention,” under which some detainees remain in custody without trial, would be continued under Afghan control. Kerry said that with Monday’s announcement the United States no longer holds any prisoners in Afghanistan.

“The transfer of the detention facility is an important part of the overall transition of security lead to Afghan National Security Forces. This ceremony highlights an increasingly confident, capable, and sovereign Afghanistan,” said Gen. Joseph Dunford, the commander of U.S. forces in Afghanistan.

At the end of last year, about 3,800 detainees remained at Parwan, only about 700 of whom were still under American control. The rate of release was significantly higher for cases adjudicated by Afghans.

Kerry’s second foreign trip as the top U.S. diplomat also took him to Iraq. In both war scarred countries, Kerry pushed a message of U.S. support while also making clear that Washington won’t call all the shots.

As a senator, Kerry traveled to Afghanistan during similarly tense moments. In 2009, he went to Kabul to urge Karzai to hold a runoff election after Karzai’s victory was seen by many as tainted by fraud. In 2010, Kerry accused Karzai of ignoring corruption in his own government, warning the Afghan president that his poor leadership could embitter both lawmakers and the families of U.S. troops.

Kerry and Karzai said they had helpful discussions about the prospect of reconciliation with the Taliban, but gave few specifics. The issue is complicated by Karzai’s demand that the Persian Gulf nation Qatar sign a memorandum of understanding that would allow for the opening of a Taliban office in Doha.

Officials in Qatar have refused to sign such an agreement, which would outline the purpose of the Taliban office and codify the Afghan government’s role in peace talks. Meanwhile, Taliban representatives are often in the city, holding unofficial meetings that U.S. officials said are sometimes constructive for wider peace talks and sometimes not.

In an apparent breakthrough, though, Karzai announced last week that he would soon travel to Qatar to discuss future Taliban negotiations. Karzai said at Monday’s press conference that his government has had recent “individual contacts” with the Taliban, which he called a step towards reconciliation.

Obama supports the opening of the political office, which would give an address for talks with the U.S.-backed government in Kabul without conferring wider legal rights on the Taliban.

Kerry had hoped to also visit Pakistan on this trip, but will delay that visit until the central government there is more settled. Elections are scheduled for May. Instead, Kerry had a hastily arranged dinner Sunday in Amman, Jordan, with Pakistan’s Army chief, Gen. Ashfaq Kayani.

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