At an emergency cabinet meeting, it described the killing of the senior Pashtun official as a "terrorist attack" and pledged to find the perpetrators.
Prayers were held at Kabul's main mosque on Sunday for Qadir, who died in a hail of bullets as his car left his office.
Afterwards his body was flown out of Kabul, accompanied by dignitaries and cabinet ministers, for burial in his home province of Nangarhar in the east of the country.
Tuesday has been declared a day of national mourning for the dead minister.
Attacks on the Afghan Government
July: Haji Abdul Qadir, vice-president and minister of public works, shot and killed
April: Four civilians die in bomb attack aimed at Defence Minister Mohammad Fahim
February: Civil Aviation Minister Abdul Rahman killed in controversial circumstances
Qadir, who was also minister for public works, had found success in the often shady world of cross-border trading and had thrown his lot in with the non-Pashtun Northern Alliance.
The Pashtun community in Afghanistan was the power base of the ousted Taleban regime and there are concerns that the assassination could destabilise the eastern provinces.
The vice president was a powerful leader there, but the central government had far less influence.
Sudden attack
Two gunmen leapt from behind bushes and sprayed dozens of bullets at Qadir's car with bullets from assault rifles at point-blank range.
The vice president was shot through the head and his driver was also killed.
The killers made their escape in a car despite a major security operation launched in the city.
A spokesman for President Karzai, himself a Pashtun, said he was upset at losing a "prominent member of his government and a Pashtun".
Leaders from Europe and the US expressed their shock at the assassination and pledged continued support for the Afghan authorities.
Qadir had powerful friends who may wish to take revenge, the BBC's Kate Clark reports from Kabul.
From Bin Laden to Bonn
Our correspondent says Qadir was a man shrouded in controversy.
He was a powerful military and political figure with vast business interests in the east of Afghanistan.
An old mujahideen commander who fought against the Taleban, he was also suspected by Western diplomats of making money out of the heroin trade.
He first achieved fame during the war against the Soviets in the 1980s.
Having made his money exporting goods to Pakistan, he was the first Afghan host to al-Qaeda leader Osama Bin Laden, letting him use a network of caves in the east after he left Sudan.
He went on to become one of the few prominent Pashtuns to join the Tajik and Uzbek-dominated Northern Alliance which fought the Taleban.
His brother, warlord Abdul Haq, was hanged by the Taleban last year when he tried to promote an uprising.
Qadir walked out of the post-war talks in Germany on the restructuring of Afghanistan, complaining that ethnic Pashtuns were not being given a big enough role.