It was not immediately known whether the loud explosions caused any damage or casualties.
The mortars were fired at about 7.15am from nearby Dora, one of the most violent areas of Baghdad, said police 1st Lieutenant Thair Mahmud.
Two large plumes of smoke could be seen rising over separate areas of the Green Zone, one white and one grey.
The blasts occurred one day after Iraq's historical constitutional referendum, and about an hour after officials had lifted one of the many security restrictions that had been enforced across the country during Saturday's vote: a ban on all civilian traffic.
A US military spokesman said he had heard and felt the explosions in the Green Zone but had no official information on them yet.
On 10 October, a car bomb exploded near a US-Iraqi checkpoint leading into the Green Zone, killing a US soldier, three Iraqi policemen and three civilians, officials said.