MoI spokesman Sediq Sediqqi said the organisation was targeted in a bombing and attackers then entered the building in Shar-e-Naw, reports Tolo News.
He added the security forces were combing the building for the gunmen but it was not known how many of them holed inside.
Sediqqi confirmed that at least one civilian was killed and one other was wounded.
Monday night at 11 pm, the attack started off with a heavy explosion, which was thought to have been a car bomb. Later, gunfire took place throughout the night.
On Monday afternoon, twin explosions outside the Ministry of Defence killed over 30 people and wounded dozens more.
The first blast took place at the gate of the ministry, followed by a suicide bomber, who targeted the first responders to the scene of the initial explosion.
A number of high ranking police and military officials were killed in the incident.