Nauert said that they were stood by the readout issued by the state department stating that Pompeo has pressed Prime Minister Imran Khan in a phone call to take "decisive action" against "terrorists" operating in Pakistan.
"Pakistan takes exception to the factually incorrect statement issued by U.S. State Dept on today's phone call", the spokesman for the Ministry of Foreign Affairs said on Twitter.
"The impression that has been given in their press release, in which they are mentioning "terrorists operating in Pakistan", is contrary to the facts with reality. This should be corrected immediately".
U.S. Secretary of State Mike Pompeo and Pakistani Prime Minister Imran Khan are seen in a combination of file photos.
Pakistan's foreign ministry called for the United States to amend its statement, but US State Department said it stands by its account.
However, according to Pakistan's Foreign Office, Mr Pompeo congratulated Imran Khan while discussing other issues of interest, but there was no mention of "terrorists operating in Pakistan".
Foreign Minister Shah Mehmood Qureshi has vowed to improve ties with the US Administration and said Pakistan needs to understand the dynamics of Afghanistan. "We hope to forge a good, productive working relationship with the new civilian government", said Nauert.
The strong rejection by the MOFA, however, failed to prompt a correction from the US State Department.
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Pakistan regularly denies that the Afghan Taliban operates from its soil.
The recent diplomatic tussle is first of the new government of Imran Khan who in his victory speech after July 25 elections had said he wants a balanced relation between Pakistan and America which should be mutually beneficial, not one sided.
Pakistani Foreign Minister Shah Mehmood Qureshi on Friday confirmed that Pompeo is scheduled to visit Pakistan on September 5.
A report seeking a ban on foreign tours of ministers, advisers and secretaries would also be presented, Geo News reported.
"The Afghan president has pointed towards a peace process and we have to see how Pakistan can help in this process", Qureshi said.
"We all need to move forward with one heart & mind, that is what we're interested in", said Kerala chief minister Pinarayi Vijayan today.
Further, Qureshi told the reporters that Pakistan was on the grey-list of the Financial Action Task Force (FATF), stating that this was not the first time this had happened.