At least 67 people, including students and teachers, were inside the centre in Jalalabad, the capital of Nangarhar province, at the time of the attack, provincial governor spokesman Attaullah Khogyani told AFP.
So far, 57 had escaped to a "safe area" but 10 were still missing, he said.
Plumes of black smoke could be seen rising from the centre and gunfire could be heard from inside.
There was no immediate claim of responsibility for the latest attack, but most of the recent assaults in the city have been carried out by the Daesh, which has a stronghold in Nangarhar.
"The Afghan security forces have cordoned off the area and launched an operation to gun down the attackers," Khogyani said earlier.
Three wounded civilians have been taken to hospital.
Provincial health department spokesman Inamullah Miakhil said 48 women from remote districts of the province were enrolled in the two-year midwifery course.
The training facility is located near the centre of Jalalabad in an area where several international organisations and consulates have offices.
A witness in a nearby department told AFP he heard several explosions and then saw three gunmen enter the street where the midwife centre is located.
Some of the security forces appeared to be dismantling improvised explosive devices apparently planted in the street by the militants, a witness told AFP.
Jalalabad has been the scene of several attacks in recent months that have killed dozens, as US and Afghan forces continue offensive operations against IS and Taliban militants.
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