"It's a personal decision" US embassy spokesman Mark Stroh was quoted as saying by CBS News. "It's not because either the Pakistani government or the US government is dissatisfied with his performance," he added.
Earlier in the day, Washington Post had said he was resigning because of his alleged differences with the Obama administration.
"Munter announced to his staff Monday morning that he was stepping down this summer after serving less than two years on the job," the Post reported, saying that the word was that he wasn't a good fit with the Pakistani government.
"Word is that Munter, a veteran career diplomat whose prior postings had been in Bonn, Prague and Warsaw and as ambassador to Serbia before becoming a senior official in Iraq in 2009 and 2010, simply wasn't a good fit with the Pakistani government -- and perhaps not with the Obama administration as well," the paper reported.
There was also speculation rife that Munter quit his job because of his differences with the Obama administration. But officials said this was not the case.
The news comes at a critical time when the US and Pakistan are believed to be having crucial negotiations on resetting of their relationship that have been hit for the last year and half.
While the Pakistani foreign ministry says a successor has yet to be formally named, an official at the ministry says Pakistani authorities have been informally told that a senior diplomat from the US embassy in neighbouring Afghanistan will likely take the position.
"We understand that Richard Olson, who is a senior US diplomat in Kabul and is looking after US aid and economy related matters, is being actively considered for the job," the official was quoted as saying by CBS News.