A "lot of work" is needed to put Pakistan-US ties back on track and Islamabad must sever its links with militant groups like the Haqqani network, Munter said in a wide-ranging interview with 'Radio Pakistan'.
"Let me tell you that the attack that took place in Kabul a few days ago, that was the work of the Haqqani network.
"And the facts, that we have said in the past, that there are problems, there is evidence linking the Haqqani network to the Pakistan government," he said in response to a question about the current state of bilateral ties.
He did not give details about the evidence.
"This is something that must stop. We have to make sure that we work together to fight terrorism.
"We have to make sure that the efforts that we are making to build the ties between our intelligence services bring about results," he said.
The US has to talk with the Pakistan government "very openly and clearly about how we can make sure" that attacks like the one in Kabul do not happen in future, Munter said.
Efforts are being made to recognise the "common enemy" of the US and Pakistan who attack people of both countries and their allies, the envoy noted.
"We have to fight these people. We cannot let events like that happened in Kabul to take place," he said.
Munter's remarks came close on the heels of a warning from Defense Secretary Leon Panetta that the US would retaliate against attacks on its forces in Afghanistan by Pakistan-based militants.
US Vice President Joe Biden too has criticised Pakistan in recent days as an unreliable ally in the war against terrorism.
Unnamed US officials were today quoted by the Wall Street Journal as saying that they are looking for evidence that directly links elements of Pakistan's military-run Inter-Services Intelligence agency to the 20-hour assault on the US Embassy in Kabul that killed 27 people in total.
Pakistan has angrily rejected the US administration's charges, saying such accusations were "out of line" with ongoing counter-terrorism cooperation between the two sides.
Munter said Pakistan and the US need to jointly fight terrorist and extremist elements and defeat them "because that will allow us to take care of those other elements that we need for long-term investments in your future".
He acknowledged that bilateral relations had been "tough" over the past year and both sides have to be realistic about "what we can expect is a good relationship".
Pakistan-US relations "today need a lot of work", he remarked.
At the same time, Munter warned that the US would defend itself against attacks by groups like the Haqqani network.
"Obviously, we are going to defend ourselves. We have always said we will, and we always have because when our soldiers are attacked, when our diplomats are attacked, we are not going to let that happen," he said.
Munter said Pakistan and the US could overcome problems in bilateral relations caused by events like the arrest of CIA contractor Raymond Davis earlier this year and the US raid that killed Osama bin Laden "if we are honest with each other and straightforward".