Pakistan is seen as critical to bringing peace to neighbouring Afghanistan, but the United States has failed to persuade it to go after militant groups it says cross the border to attack Western forces in Afghanistan.
"This is not helping either the United States, Afghanistan or Pakistan," Salim Saifullah told Reuters.
"There will be pressure on the (Pakistan) government to get out of this war," he said, referring to the US war on militancy.
Obama warned Pakistan on Thursday that its ties with "unsavory characters" have put relations with the United States at risk, as he ratcheted up pressure on Islamabad to cut links with militants mounting attacks in Afghanistan.
He accused Pakistan's leaders of "hedging their bets" on Afghanistan's future, but stopped short of threatening to cut off US aid, despite calls from lawmakers for a tougher line over accusations that Pakistani intelligence supported strikes on U.S. targets in Afghanistan.
Saifullah said Washington's public criticism of Pakistan was counter-productive and would only create tensions between allies that would play into the hands of militant groups.
"War in Afghanistan is passing through a critical phase, evolutionary phase, at this stage muddying water is not appropriate," he said. "This is exactly what the militants want. They are playing to their tune. This is adding strength to them."
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