Humayun had links to a network led by Siraj Haqqani, intelligence officials said after the Serena attack that killed eight people.
Afghan officials say Haqqani is based in Pakistan’s tribal region of North Waziristan.
The US military has a $200,000 bounty out on him. His network is associated with Taliban and is also believed to have links to al-Qaeda members.
It is part of a myriad of groups supporting Afghanistan’s former hardline Islamist regime and bent on toppling Karzai’s Western-backed government.
“There (is) very, very strong evidence suggesting that Pakistan’s soil once again has been used to inflict pain on our nation”
Amrullah Saleh, Afghan intelligence chief
Amrullah Saleh, the intelligence chief, said those killed in the raid on Wednesday – and three other gunmen who tried to assassinate Karzai on Sunday – were all in contact with fighters inside Pakistan’s tribal regions, including in North Waziristan.
“We have no evidence whether … the operation has had any mercy or go-ahead from the government of Pakistan and (its) special agencies,” Saleh said on Wednesday.
“There (is) very, very strong evidence suggesting that Pakistan’s soil once again has been used to inflict pain on our nation.”
Although not directly implicating Pakistan’s government, Saleh’s comments will irk Islamabad and could dampen recently improved relations between the two countries.
Relations are often strained over allegations that Pakistan helps the Taliban and other groups.
Major General Athar Abbas, a Pakistani army spokesman, called the allegation “baseless”.
“Anybody can say that militants (in the tribal areas) have done this or that,” Abbas said. “How can one validate such claims?”
The Taliban, ousted from power by the 2001 US-led invasion, has claimed responsibility for the attempt on Karzai.
Afghan legislators passed a vote of no-confidence on Tuesday against the country’s three top security officials, including Saleh. They had revealed they were aware of the assassination plot against Karzai but failed to stop it.
The officials, however, retained their jobs.