Jalaluddin Haqqani, founder of the militant group the Haqqani network, speaks during an interview in Miram Shah, Pakistan, on Aug. 22, 1998. (MOHAMMED RIAZ/Associated Press)

The Pentagon has withheld $300 million in military assistance to Pakistan, U.S. officials said Wednesday, a potential blow to U.S.-Pakistani ties and a sign of ongoing frustration with Islamabad for not acting against militants fueling violence in Afghanistan.

Adam Stump, a Pentagon spokesman, said that Defense Secretary Ashton B. Carter had decided against making a certification to Congress stating that Pakistan is taking sufficient action against the Haqqani network, a Taliban affiliate blamed for attacks on U.S. and allied personnel in Afghanistan.

Stump said the decision, which means Pakistan will not receive $300 million in military reimbursement funding, was based on the continuing operations of the Afghan Taliban and Haqqani militants on Pakistani soil.

The move ends a year of speculation about an aid program that has been fundamental to Pakistani military operations, and reveals the strains in Washington’s relations with an ally that many officials have accused of double-dealing with militant groups.

The decision comes as the Obama administration grapples with deteriorating security in Afghanistan, where a resurgence in Taliban activity has derailed plans to definitively end the long military effort there.

It is the first time the Obama administration has withheld military aid to Pakistan because of the Haqqani group, which has been a primary source of U.S. concern in Afghanistan and which in the past some U.S. officials have asserted had links to Pakistani intelligence.

Carter’s decision has not been previously reported.

Shamila Chaudhary, a former White House official and senior fellow at New America, a Washington think tank, said the decision could foreshadow additional steps increasing pressure on Pakistan to crack down on militants causing trouble in Afghanistan.

“It is a way of sending a signal to the Pakistani military of what’s to come, in the sense that the United States is no longer willing to give blank checks to Pakistan,” she said.

Under the Coalition Support Funds (CSF) program, the United States reimburses Pakistan for its support of U.S. and allied operations in Afghanistan and helps Pakistan pay for operations it conducts against militants on its soil.

Since 2002, reimbursements under the program have totaled about $14 billion, representing a significant portion of Pakistan’s defense spending. In addition to helping fund operations, Pakistan’s military also used the money to buy food and ammunition, the Pentagon has said.

Nadeem Hotiana, a spokesman for the Pakistani Embassy in Washington, said the CSF program had allowed the United States to support Pakistani military actions, particularly in the country’s restive tribal areas, that had benefited both countries.

“Pakistan will continue to work with its partners in a long-term effort for ensuring security and stability in these areas,” he said.

The CSF program is an important element of the massive assistance package that Pakistan has received each year since the attacks of Sept. 11, 2001, much of it focused on securing Pakistani support for U.S. operations in Afghanistan.

In that time, though, U.S. ties with Islamabad have been rocky, as officials have struggled to negotiate tensions over CIA drone strikes and the belief of many U.S. officials that Pakistan has allowed certain militant groups, including the Haqqanis and the Afghan Taliban, to shelter in its western tribal region.

The Haqqani network, named for former anti-Soviet resistance leader Jalaluddin Haqqani, is blamed for some of the boldest attacks on U.S. targets in Afghanistan, including a 2011 assault on the U.S. Embassy in Kabul.

Washington’s ties with Pakistan grew particularly strained after the United States secretly launched the raid that killed al-Qaeda leader Osama bin Laden in 2011. Later that year, the Obama administration temporarily suspended $800 million in security aid.

Although tensions have eased since then, a stark reminder of the reasons for bilateral friction came this May, when a U.S. drone killed Taliban leader Akhtar Mohammad Mansour on Pakistani soil. Pakistan, which has been the target of repeated militant attacks, has denied support for extremist groups.

Seeking to increase pressure on Pakistan, Congress introduced new requirements related to the Haqqani network in annual defense legislation beginning in fiscal 2015. Earlier this year, lawmakers also blocked Pakistan from using another pool of U.S. military aid to buy American F-16 jets.

Before Carter’s decision to withhold the certification, the United States already had reimbursed $700 million in fiscal 2015. Chaudhary said the U.S. support was crucial for Pakistan, which does not receive such generous military aid from other allies.

“The Pakistani military is the one that loses out,” she said. “This money has been helping them for well over a decade now.”

Pentagon officials said the CSF decision was not meant to repudiate other actions that Pakistan has taken against militants, including a major military operation launched in 2014 in North Waziristan.

Hotiana said that Pakistan had cleared that area of militants from a range of groups, at great cost to its people and armed forces. “Pakistan will continue its fight against terrorism and ensure that areas cleared by the security forces do not slide back into the control of terrorist networks,” he said. U.S. officials contend that Pakistan’s actions have mostly targeted groups threatening the Pakistani state, and are not active in Afghanistan.

A senior defense official, who spoke on the condition of anonymity because he was not authorized to discuss the matter publicly, said the Pentagon had informed Pakistan of Carter’s move to deny a portion of the CSF funding.

Lawmakers also have moved to increase the carve-out subject to the same certification requirement. In a law passed for fiscal 2016, it stands at $350 million.

“The message to the Pakistanis is a lot like the message to lots of people in this whole counterterrorism realm: We always need to look for more that we can do,” the official said.

A senior staff member at the House Armed Services Committee, which oversees annual defense legislation, said Pakistan’s actions against militants were even more important as the U.S. military footprint grows smaller in Afghanistan.

“We are very focused on making sure that the appropriate incentives are out there in making sure Pakistan acts in a manner that is consistent with both of our national security interests, and certainly with ours,” the staff member said.

While Afghan troops are doing the bulk of the fighting against the Taliban, the United States plans to leave a force of 8,400 troops in Afghanistan when President Obama steps down next year.