The United States will sign a Bilateral Security Agreement, or BSA, with the Afghan government on Tuesday, just a day after Ashraf Ghani took charge from Hamid Karzai as the country's president. The BSA will allow a relatively small contingent of American troops to remain in the country after the end of the year, according to media reports.

The deal will “enable Afghanistan, the United States, and the international community to maintain the partnership…established to ensure Afghanistan maintains and extends the gains of the past decade,” U.S. State Department spokesperson Jen Psaki said on Monday.

The BSA reportedly allows a force of 9,800 U.S. troops to remain in Afghanistan after the end of 2014. Additional troops from Germany, Italy and other NATO member nations -- to be finalized under a separate agreement with NATO -- will also join the U.S. soldiers, bringing the total up to nearly 12,500, Al Jazeera reported.

As of now, there are about 41,000 NATO troops stationed in Afghanistan, according to media reports.

“The signing sends the message that President Ghani fulfils his commitments. He promised it would be signed the day after inauguration, and it will be,” Daoud Sultanzoy, a senior aide to the new president of Afghanistan, reportedly told media on Tuesday. “We are replacing uncertainty with certainty.”

Hamid Karzai, who served as Afghanistan’s president since 2004, had, during his term, refused to sign the security deal with the U.S., further straining ties between the two countries. Both Ghani and his erstwhile rival Abdullah Abdullah, however, had made signing of the deal a key campaign issue.

Meanwhile, the imminent withdrawal of most of the NATO troops from Afghanistan has also raised concerns over the fate of prisoners being held by U.S. forces in a prison near Bagram airfield in northeastern Afghanistan, according to a Reuters report.

The prisoners, which include individuals from Pakistan, Yemen, Russia and Saudi Arabia, were reportedly arrested in the aftermath of the 9/11 attacks, and have remained in U.S. custody ever since.

“We've got to resolve their fate by either returning them to their home country or turning them over to the Afghans for prosecution or any other number of ways that the Department of Defense has to resolve,” Brigadier General Patrick J. Reinert of the U.S. Army told Reuters.

However, Reinert added that it would not be possible to repatriate the incarcerated individuals until their home countries provided an assurance that the released prisoners would not be mistreated. “Until the country provides assurances, the individual cannot be transferred,” Reinert told Reuters.