Such certification is necessary in order to enable Pakistan to receive reimbursement of "Coalition Support Funds" for 2016. The funds are used to reimburse Pakistan for the cost of military operations against terrorist groups during 2016.
There was about $50 million remaining in the funds, which will now be repurposed the Pentagon said.
"The funds could not be released to the Government of Pakistan at this time because the secretary could not certify that Pakistan has taken sufficient action against the Haqqani Network per the requirement in the FY 2016 National Defense Authorization Act (NDAA)," Pentagon spokesman Adam Stump told CNN in a statement.
While many analysts believe that a tougher line on Pakistan for its connections to the Haqqani Network will be part of the administration's new strategy for Afghanistan and the wider region, the Pentagon said that Friday's announcement was unrelated to the wider review.
"This decision does not prejudge the conclusions of the White House review of South Asia strategy, which is still ongoing," Stump said.
This is the second time these funds have been withheld from Islamabad. Mattis' predecessor, Ash Carter, similarly refused to certify Pakistan was adequately combating the Haqqani Network causing Congress to withhold $300 million in funding.
Pakistan has already been reimbursed $550 million for operations against other terror groups during 2016.
"This decision does not reduce the significance of the sacrifices that the Pakistani military has undertaken over previous years," Stump said, adding that the US continues "to be encouraged by Pakistan's operations in North Waziristan and elsewhere in the Federally Administered Tribal Areas."
"However, the Taliban and the Haqqani Network continue to operate in other locations in Pakistan," Stump added.
The Haqqani Network is considered to be the most capable and violent branch of the Afghan Taliban. US officials have told CNN that the Haqqani Network was likely behind the deadly May bombing in Kabul
that killed close to 100 people.
US officials believe that much of the Haqqani leadership is based in Pakistan and some analysts believe eliminating their safe havens is critical to stabilizing Afghanistan.
The Pentagon highlighted that Pakistan could still receive reimbursement funding for operations in 2017, some $400 million, should the Pakistani military launch offensives against the Haqqani Network.
"Pakistan still has time to take action against the Haqqani Network in order to influence the Secretary's certification decision in FY17," Stump said.
Pakistan is the largest recipient of Coalition Support Fund reimbursements, having received more than $14 billion since 2002, according to the Pentagon.