Guillaume Ngefa said two burial sites had been found in a suburb of Abidjan.
He said local people allege that many of the victims were killed by former President Laurent Gbagbo's supporters.
They said the massacre in the Yopougon district happened the day after Mr Gbagbo was seized by supporters of his opponent, President Alassane Ouattara.
Football fieldMr Ngefa said the UN was examining all mass graves, including those alleged to contain the bodies of Mr Gbagbo's supporters.
The UN had announced on Friday its investigators were heading to a suspected mass grave site at a football pitch in Yopougon.
Last month, UN investigators found at least 200 bodies in a mass grave in the western Ivorian town of Duekoue.
In January, as the political violence escalated, UN high commissioner for human rights Navi Pillay said Gbagbo loyalists had denied her officials access to three mass graves in the country.
Mr Ouattara, Ivory Coast's internationally recognised president, was sworn in last week.
Mr Gbagbo's refusal to cede power after losing a November election sent the nation close to repeat of its 2002-03 civil war.
He is now under house arrest and is being investigated for alleged human rights abuses.
Some 3,000 people are believed to have been killed during the unrest in the world's largest cocoa producer, previously one of West Africa's richest countries.
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