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President Barack Obama cast some doubt on the long-term relationship between the United States and Pakistan on Thursday, saying his administration was concerned about the Pakistani government’s commitment to U.S. interests because of ties between anti-U.S. militants in Afghanistan and Pakistan’s own intelligence service.

At a news conference in Washington focused mostly on the U.S. economy, Obama said he was thankful for cooperation from Pakistan, which has allowed the United States to use drones to strike at al-Qaida cells ensconced along the Pakistan-Afghanistan frontier. But he also obliquely criticized Pakistan over its position regarding Afghanistan, where efforts to stabilize the country and wind down the U.S.-led war have been frustrated by what U.S. and Afghan officials have described as Pakistan’s support for insurgent groups, including the Taliban and their allies in the Haqqani network.

“I think that they have hedged their bets in terms of what Afghanistan would look like,” Obama said. “And part of hedging their bets is having interactions with some of the unsavory characters who they think might end up regaining power in Afghanistan after coalition forces have left.”

The United States would “constantly evaluate” Pakistan’s cooperation, Obama said. He added: “But there’s no doubt that, you know, we’re not going to feel comfortable with a long-term strategic relationship with Pakistan if we don’t think that they’re mindful of our interests as well.”

Obama’s remarks seemed to call into question whether the United States could continue supplying Pakistan with billions of dollars in military and civilian aid, as it has since the Sept. 11, 2001, attacks, if its intelligence service could not be persuaded to drop its support for militant groups long used as proxies against India and Afghanistan.

Asked, however, if he would be willing to cut off aid to Pakistan, recently ravaged by flooding, Obama hesitated. The United States had a “great desire to help the Pakistani people strengthen their own society and their own government,” he said. “And so, you know, I’d be hesitant to punish flood victims in Pakistan because of poor decisions by their intelligence services.”

His remarks came against a backdrop of already heightened U.S. tensions with Pakistan, since Adm. Mike Mullen, the just-retired chairman of the Joint Chiefs of Staff, told a Senate panel last month that the Haqqani network, a potent part of the insurgency battling U.S. forces in Afghanistan, was a “veritable arm” of Pakistan’s spy agency. Mullen also accused the agency of supporting an attack by Haqqani militants on the U.S. Embassy in Kabul, the Afghan capital.