Interior Ministry spokesman Sediq Sediqqi tweeted that 64 "innocent Afghans" were killed and 347 wounded.
A suicide attacker detonated a vehicle and a fierce gun battle followed in one of the deadliest attacks in Kabul for years.
A Taliban spokesman said the group carried out the attack.
It came a week after it said it was launching its "spring offensive", warning of large-scale attacks, although the group fights all year round.
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Tuesday's bombing happened during the morning rush hour in Pul-e-Mahmud, a busy neighbourhood where homes, mosques, schools and businesses nestle close to the ministry of defence, other ministries and military compounds.
The blast shattered windows up to 1.6km (one mile) away. A police officer told the Associated Press it was one of the most powerful explosions he had ever heard, and he could not see or hear anything for 20 minutes after.
It appears the initial blast cleared the way for Taliban fighters to enter the area - a commonly used tactic.
It had previously been reported that at least 28 people had been killed and 329 injured.
Mr Sediqqi told reporters that most of the 64 now reported dead were civilians. He said most of the wounded were in a stable condition.
At least 71 Shia worshippers were killed in 2011 in a rare attack on a Shia shrine in Kabul.
Afghan security forces regularly foil similar attacks, correspondents say, but with explosives easily available and bomb-making skills common, it is difficult to prevent all of them.
The death toll from a huge explosion in the centre of the Afghan capital Kabul on Tuesday has more than doubled to 64 people, the government says.