A lot of them were killed during prayer in mosques or religious ceremonies, according to an United Nations report released last week.
The first explosion rocked Imam Zaman mosque in the western district of Dasht-e-Barchi in the Afghan capital, Kabul, on Friday as worshipers had gathered for prayers.
The explosion occurred at around 6:30pm when the worshippers were doing the evening prayer.
Two auto bombs exploded at the gate of the police headquarters, Danish said.
According to an eyewitness, women and children were also among the victims of the attack.
Interior ministry spokesman Najib Danish confirmed the latest attack toll on Twitter.
Security forces cordoned off the area for precautionary measures.More news: Katy Perry gets stuck mid-air on planet prop during concert
"We wish Allah's mercy upon those who lost their lives, a speedy recovery to the wounded, and convey our condolences to the brotherly government and people of Afghanistan".
Many people were chanting slogans against insurgents outside the mosque few hours after the attack.
The second blast targeted a mosque in the central province of Ghor, leaving at least 20 people dead, said Iqbal Nezami, a spokesman for the Ghor provincial police.
There was no immediate claim of responsibility for the attacks but recent assaults on Shia mosques have been carried out by the Islamic State of Iraq and the Levant (ISIL) group.
Afghan President Ashraf Ghani condemned the mosque attacks as "crimes against humanity".
On Tuesday, at least 41 people were killed and scores were injured in an attack on police headquarters in the Paktia provincial capital of Gardez, located in eastern Afghanistan.