"Munter announced to his staff Monday morning that he was stepping down this summer after serving less than two years on the job," the Washington Post reported, saying that the word was that he wasn't a good fit with the Pakistani government.
Normally ambassadors usually serve three-year tours and Munter has only been in Islamabad since October 2010.
"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.