"We learned with sorrow that many were killed and more wounded in attacks at mosques in the Kabul and Ghor provinces of Afghanistan, today", the Foreign Ministry said in a statement.
Ashraf Ghani says that the day's attacks show that "the terrorists have once again staged bloody attacks but they will not achieve their evil purposes and sow discord among the Afghans".
No group immediately took credit for the attack, but the Islamic State militant group has recently claimed responsibility for similar attacks.
Security forces cordoned off the area for precautionary measures.
Police initially said a gunman entered the Imam Zaman mosque in a heavily Shiite neighbourhood in the west of the city and opened fire on worshippers.
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About an hour before the blast in Kabul, a suicide attacker detonated explosives at the Khwajagan mosque in the Du-Layna district of Ghor province. At least 10 people reportedly were killed in that incident.
A suicide bomber set off his explosives inside a mosque in the Afghan capital on Friday, officials said, killing at least 30. Seven of his bodyguards were also killed in the attack.
"The explosion happened when the worshippers were inside the mosque", the Khaama Press quoted Ghor governor's spokesman Abdul Hai Khatibi as saying.
No group has so far claimed responsibility for either attack.