KABUL, Afghanistan — Afghanistan’s new government took a big step toward rebuilding relations with Washington, signing a long-delayed security deal on Tuesday that sets the terms for nearly 10,000 U.S. troops to remain past the December deadline for the withdrawal of coalition combat forces.

U.S. leaders swiftly welcomed the signing of the deal and hailed it as heralding a continuing partnership to defeat al-Qaida and their insurgent supporters.

Hanif Atmar, Afghanistan’s national security adviser and former interior minister, inked the accord for the Kabul government. Ambassador James Cunningham signed on behalf of the United States.

The ceremony took place in a gilded hall in the presidential palace, with flags of Afghanistan, the U.S. and NATO framing the dignitaries. In attendance were the new Afghan president, Ashraf Ghani, and his rival and runner-up in the election, Abdullah Abdullah, who now serves as a chief executive officer in the new unity government, just a day after both took office. Their presence underscored the importance of the signing, and their commitment to the partnership with the U.S. and NATO.

The relationship between Kabul and Washington had frayed in the months since former Afghan President Hamid Karzai last year backed down on a pledge to sign the deal, leaving that task to his successor.

NATO representatives signed a separate Status of Forces agreement to allow a contingent of 2,000-3,000 allied troops to join some 9,800 U.S. forces in training and advising the Afghan security forces in 2015.

Some of the 9,800 American troops will conduct counterterrorism missions, but “the vast majority” will be dedicated to the train and advise effort, a senior State Department official told reporters during a conference call on Tuesday.

The official, who agreed to speak to the press on condition of anonymity, declined to say precisely how many U.S. troops will be focused on counterterrorism.

When asked what kind of enablers the U.S. will provide to the Afghan security forces going forward, and whether the U.S. personnel involved in those efforts would count towards the 9,800 troop cap, the official said: “The issue of enablers for Afghan operations is still a matter of discussion within the administration. But if there were to be such support, my expectation is it would come from within the 9,800.”

Enablers include things like air support and intelligence assistance.

There is no timeline for making that decision, according to the official.

Leaders on both sides hailed the agreements as a chance to put their relationship on a new footing as the NATO-led coalition prepares to end its combat operations at year’s end.

“We have signed this looking to the needs of Afghanistan, and the needs of the international community,” Ghani said during the ceremony. “It is a very balanced agreement.”

President Barack Obama called the deal an “invitation from the Afghan Government to strengthen the relationship we have built over the past 13 years.”

“The BSA reflects our continued commitment to support the new Afghan Unity Government, and we look forward to working with this new government to cement an enduring partnership that strengthens Afghan sovereignty, stability, unity and prosperity, and that contributes to our shared goal of defeating al-Qaida and its extremist affiliates,” he said in a statement released by the White House.

Referring to the BSA as “an important step forward,” Defense Secretary Chuck Hagel said in a statement that “these agreements will enable American and coalition troops to continue to help strengthen Afghan forces, counter terrorist threats and advance regional security.”

Both Obama and Hagel paid tribute to the work of American troops during more than a decade of war in Afghanistan.

“This day was only possible because of the extraordinary service of our men and women in uniform who continue to sacrifice so much in Afghanistan on behalf of our security and the Afghan people,” Obama said. “The American people are eternally grateful for their efforts.”

The security accord is critical to the continuing presence of U.S. and international troops because it lays out key requirements, including the exemption of U.S. troops from prosecution in Afghan courts. Failure to reach such an agreement in Iraq led to the full withdrawal of all U.S. forces from there in 2011.

The U.S. has been keen to maintain a small force, primarily to advise and assist Afghan security forces so they can stave off persistent attacks from Taliban militants and ensure that 13 years of war and lost lives were not for naught.

“This agreement was concluded to ensure the peace, stability and defense of Afghanistan,” Ghani said. “If our territory faces a serious threat or danger, according to the agreement we can ask the United States and NATO for help so that we can face that danger together.”

Cunningham said the two countries had made great progress in bringing stability to Afghanistan.

“Our close defense and security cooperation will provide the foundation for Afghanistan to continue its impressive development and to build on the achievements of the past (and) also contribute to stability not only in Afghanistan, but throughout the region,” he said.

NATO’s outgoing secretary-general, Anders Fogh Rasmussen, also hailed the agreement in a statement released from Brussels. He said the new NATO-led mission, called Resolute Support, could start as planned on Jan. 1.

“The conclusion of these agreements opens a new chapter for cooperation between NATO, our partners and the Afghan National Security Forces,” Rasmussen said on the last day of his tenure.

The signing ceremony came just a day after Ghani was sworn in to replace Hamid Karzai. Karzai had refused to sign the accord, even after a Loya Jirga — or counsel of elders and key officials from across the country — overwhelmingly encouraged him to do so last November.

In September, the U.S.-led coalition still had 41,000 troops in Afghanistan — two-thirds of them Americans. This is down from a peak of more than 140,000 three years ago.

In the conference call on Tuesday, the official acknowledged that the drawdown will inevitably make it more difficult for the U.S. to go after terrorists in Afghanistan.

“With a smaller footprint and fewer people, you do less than with a larger footprint and more people,” the official told reporters.

In the past, the U.S. has used Afghan soil to launch attacks against militants in neighboring Pakistan, most famously in the raid that killed Osama bin Laden. The official said the counterterrorism provisions in the new security agreement only apply to counterterrorism operations conducted within Afghanistan.

Zubair Babakarkhail contributed to this report. Stars and Stripes Pentagon reporter Jon Harper also contributed to this report.

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