"As all of us have hoped for many, many years - we have hoped that Pakistani leaders will understand that it is in their interest to go after these groups less selectively than they have in the past," Lt Gen McMaster said during his latest visit to Afghanistan, according to a report in The New York Times.
"The best way to pursue their interests in Afghanistan and elsewhere is through the use of diplomacy, and not through the use of proxies that engage in violence," it quoted him as saying.
The report added that Afghan officials are aware of the discussions with Lt Gen McMaster saying there was a common understanding of the threat of terrorist groups emerging from Pakistan.
"And there are other indications that the United States may be weighing a tougher stance on Pakistan, among them General McMaster's reported pick of a point person on the country who has strongly advocated that the United States stop treating Pakistan as an ally and condition any future military aid on fighting terrorist groups," the report added.
It said many analysts, as well as some coalition partners, have been critical of the United States' uphill struggle to persuade Pakistan to crack down on the Afghan Taliban leadership, which has used Pakistan as a base for its battles in Afghanistan.
"Many people in Afghanistan are wondering about the nature of relations between the United States and Pakistan, particularly the fact that everyone recognisers the principal role of Pakistan in supporting Taliban and other terrorist groups," said Davood Moradian, the director of the Afghan Institute for Strategic Studies.
Mr Moradian said the new administration realised that the prior "appeasement policy" with Pakistan had not worked and needed to be reconsidered.