They landed in the district of Abobo, which is under the control of militias who back his rival, Alassane Ouattara.
Mr Gbagbo refuses to step down although Mr Ouattara is widely recognised as the winner of last year's poll.
A statement from the UN mission in Ivory Coast says that about 100 people were killed or maimed by at least six 81mm mortar shells.
"Such an act, perpetrated against civilians, could constitute a crime against humanity," it says.
But Ahoua Don Mello, a spokesman for Mr Gbagbo's government, told the AFP news agency the accusations against the security forces were part of a "conspiracy" between the UN, Mr Ouattara's supporters and former colonial power France to oust Mr Gbagbo.
Mr Mello later read out a statement on national TV, saying Mr Gbagbo was open to talks as part of an African Union peace plan.
He also accused regional powerhouse Nigeria of transporting 500 mercenaries to pro-Ouattara forces based in the northern town of Bouake.
Pro-Gbagbo forces have been accused of firing at peaceful demonstrators on several occasions recently.
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