The Haqqani network has carried out a number of kidnappings and attacks against US interests in Afghanistan, the Afghan government and other civilian targets.
The group is also blamed for several deadly attacks against Indian interests in Afghanistan including the 2008 bombing of the Indian mission in Kabul that killed 58 people.
The Pentagon said it was in Pakistan's interest to take action against terrorists in "as many ways as possible".
"We continue to have a close relationship with Pakistan with regard to terrorism and fighting terrorism. (But) It's obviously in Pakistan's own interest and the United States interest to combat terrorism in as many ways as possible," Pentagon Press Secretary Peter Cook told reporters on Monday.
US Defence Secretary Ashton Carter did not give Congressional certification to Pakistan for satisfactory action against the Haqqani network this year, Cook said.
In the absence of the certification, the Pentagon blocked disbursement of $300 million to Pakistan under coalition support fund, which is essentially reimbursement money for the expenses made by Pakistan Army in support of US operations in Afghanistan.
"With regard to that $300 million, there was a (June 30) deadline in terms of whether or not to transfer that money or to use that money in other ways, and it was determined that at this moment in time, it was best to reprogramme that money in other directions," Cook said.
The Washington Post has described the withholding of the US military assistance to Pakistan as a "potential blow" to US-Pak ties.
The Pentagon press secretary, however, said the US will continue to work "closely with Pakistan and we've seen significant efforts on the part of the Pakistanis."
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