According to witnesses, gunmen entered the Karte Sakhi shrine near Kabul University late yesterday, firing "indiscriminately" on men, women and children as they tried to flee.
The UN in Afghanistan called the attack an "atrocity" and put the toll at 18 today.
But the interior ministry later said in a statement that 16 people including three women and two children were killed and 54 wounded in two separate attacks in Kabul yesterday night.
At the same time, another attacker entered a nearby mosque and took an unspecified number of people hostage as they were commemorating Ashura.
Both attackers were killed by Afghan security forces and the hostages were released, the statement said, without clarifying if any casualties were sustained in the second assault.
In a Kabul hospital today, victims wounded in the attack on the shrine said more than one gunman was involved in the attack.
One mother who gave her name as Saleha told AFP of a gunman who was "killing everyone".
"While I was hugging my little son I begged him not to kill my child," she said.
The child survived, but she angrily denounced the Afghan government for failing to protect them.
"The families of the president, CEO Dr. Abdullah and other rich ones live abroad. Here, only poor people are killed every day."
Another witness, Ali Hussain, said attackers wearing military uniforms first shot the police guard at the gate and then entered the shrine, where dozens of worshippers had gathered.
"They indiscriminately shot everyone they faced. They wouldn't even spare women and children," said Hussain, who fled through a library back door.
The Taliban said they were not involved and no group has yet officially claimed responsibility for what President Ashraf Ghani condemned as a "clear sign of a crime against humanity".
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