Mattis, on a one-day visit to Pakistan, said the South Asian nation had made progress in the fight against militancy inside its borders but needed to make more.
The US has repeatedly accused Pakistan of not doing enough to eliminate militant havens on its territory.
“Hopefully, there will be a change in the cooperative relationship between the United States and Pakistan,” White House chief of staff John Kelly said after the rescue operation.
“You want us to sniff them out, we will do that. You want us to take action against them, whatever action you propose, we will do that… (but) these hollow allegations are not acceptable.”
Relations between the two countries have been frayed over the past decade as officials have long questioned the role Pakistan has played in Afghanistan.
If implemented, the new policy will likely lead to confrontation with nuclear-armed Pakistan, but that does not mean the US should shy away from holding Islamabad’s feet to the fire.
In a clear articulation of a new Afghan policy, James Mattis and Rex Tillerson have virtually ruled out any political settlement with the Taliban.
US patience with Pakistan appears to have finally run out. But whether this will mean Washington will try something different with Pakistan remains to be seen.
Engaging and enticing Pakistan into giving up its jihadist adventure in Afghanistan has let the country believe it can get away with harbouring terrorists.
A new report by US-based experts has called for the Trump administration to take a tougher stand against Pakistan to urge it to turn its back on terrorist groups.
The National Defence Authorisation Act imposes four conditions on Pakistan to be eligible for the $400 mn – all centred on Islamabad significantly targeting the Haqqani network.
If New Delhi chooses not to act as a bridge between Washington and Kabul, it will have to shoulder more responsibilities in Afghanistan on its own, for which it is unprepared.
The decision by the Pentagon is a sign that while it sees some progress by Pakistan in its military operations in North Waziristan, much work remains.
The planes, which were to be a parting gift from the Obama administration to the Pakistani military became a symbol of all that is wrong with US policy on Pakistan.