The Trump administration announced on Thursday that it would suspend nearly all security aid to Pakistan, an across-the-board freeze that is the most tangible sign yet of Washington’s frustration with the country’s refusal to crack down on terrorist networks operating there.
The decision, which could affect as much as $1.3 billion in annual aid, came three days after President Trump complained on Twitter that Pakistan had “given us nothing but lies & deceit” and accused it of providing “safe haven to the terrorists we hunt in Afghanistan.”
The move underlines how swiftly relations with Pakistan have deteriorated since Mr. Trump took office. But it echoes several previous rifts between the countries over Pakistan’s role as a sanctuary for extremist groups — a role that has poisoned Islamabad’s relations with Washington since the terrorist attacks of September 2001.
Administration officials emphasized that the freeze was temporary and could be lifted if Pakistan changed its behavior. The United States is urging the Pakistani government to cut off contact with militants and reassign intelligence agents with links to extremists, among other measures.
United States officials had also demanded access to a member of the Taliban-linked Haqqani network, who was captured by Pakistani forces during the rescue of a Canadian-American family in October, and were angered when Pakistan rejected the request.
“It’s hard to argue the status quo has been working, so we are looking at changing it to advance our security objectives,” said Brian H. Hook, the State Department’s director of policy planning.
Heather Nauert, the department’s spokeswoman, said the administration was still working out the precise dollar amounts that would be frozen. Though the move was months in the planning, officials said the announcement was rushed by a few days to catch up to Mr. Trump’s Twitter post on Monday, which drew a toxic reaction from Pakistan.
The move also came after considerable internal debate, officials said. The Pentagon is worried that the Pakistani government could retaliate by denying access to routes in Pakistan that it uses to supply roughly 14,000 American troops deployed in neighboring Afghanistan.
After Mr. Trump’s tweet, the foreign minister of Pakistan, Khawaja Muhammad Asif, said that there was a need to revisit the nature of its relations with the United States. In an interview with a local news network, he said the United States was acting like neither an ally nor a friend.
The suspension includes about $1.1 billion in Coalition Support Funds, which the Pentagon provides to help defray the costs of counterterrorism operations in Pakistan. Under the freeze, the United States also will not deliver military equipment to the country. It had earlier held up $255 million in State Department military financing.
Ms. Nauert said some exceptions could be made “on a case-by-case basis if determined to be critical to national security interests.” Internal government talking points that were obtained by The New York Times said the suspension was “a freeze, and does not reflect intent to reprogram funds at this time” — meaning that the money will not be diverted to other uses.
“Pakistan has the ability to get this money back in the future, but they have to take decisive action,” Ms. Nauert said.
The administration said that the freeze did not apply to civilian assistance programs. The United States has provided Pakistan more than $33 billion in aid since 2002, a program that ramped up sharply in the wake of the Sept. 11 attacks as the United States viewed Pakistan as a key ally in fighting Islamic militants.
Earlier on Thursday, the State Department announced that it had placed Pakistan on a special watch list for what it described as severe violations of religious freedoms. The designation was part of the administration’s annual accounting of violations by countries as required by the International Religious Freedom Act of 1998.
Attacks on religious minorities have increased in Pakistan in recent years, reflecting a growing religious intolerance and driven in part by a proliferation of religious schools funded by Saudi Arabia.
The United States previously has frozen military aid without forcing a change in Pakistan’s policies. In July 2011, two months after an American commando raid that killed Osama bin Laden in Pakistan, the Obama administration suspended about $800 million in aid. Relations with Pakistan did not improve, and officials there have come to discount such threats.
“This is a great opening salvo, but I don’t think it is enough to make Pakistan change its behavior, unless we have a Plan B,” said C. Christine Fair, a professor who specializes in South Asia at the security studies program at Georgetown University.
Still, Ms. Fair said the scale of the administration’s action suggested it was serious about forcing a change. White House officials said they would consider further steps, including removing Pakistan from a list of major non-NATO allies of the United States — a move that would carry enormous symbolic significance for the relationship.
Husain Haqqani, a former Pakistani ambassador to the United States, said the decision “indicates that the administration does have a step-by-step plan to indicate to Pakistan that business as usual is no longer possible.”
While Mr. Haqqani said that Pakistan might well retaliate by shutting off ground supply routes to Afghanistan, such a move would also carry costs for the Pakistanis, since they supply many of the trucks and other logistics for the supply operation.
Defense Secretary Jim Mattis, speaking to reporters on Thursday, said, “We have had no indication of anything like that.”
The administration has augured the freeze ever since Mr. Trump announced his Afghanistan strategy over the summer, in which he faulted Pakistan for failing to crack down on terrorist sanctuaries that line the border between the two countries. His language grew harsher in recent weeks. Last month, in presenting his national security strategy, Mr. Trump again singled out Pakistan. “We make massive payments every year to Pakistan,” he said. “They have to help.”
Vice President Mike Pence reinforced that message in a visit to Afghanistan just before Christmas, telling cheering American troops that “President Trump has put Pakistan on notice.”
But some analysts argued that while publicly complaining about Pakistan’s lack of action against terrorist groups may feel satisfying, such accusations were deeply counterproductive.
Richard G. Olson, a former special representative for Afghanistan and Pakistan during the Obama administration, noted that the American military effort in Afghanistan was heavily reliant on Pakistan’s consent. Almost every military flight into Afghanistan, including those of attack aircraft, goes through Pakistani airspace. Most supplies travel along Pakistani roads and rails.
“Our choices in Afghanistan are already difficult, but if you want to make them even more difficult, continue to taunt the Pakistanis,” Mr. Olson said. “The Pakistanis could effectively shut down the war.”
Pakistan closed ground supply routes to Afghanistan in the months after the raid that killed Bin Laden, and those supply lines were rerouted to the northern route. But the northern route is heavily dependent on Russian consent, and with relations between Washington and Moscow deteriorating, such consent is far from assured.