Human rights groups say Amade Oueremi's fighters executed hundreds of supporters of former President Laurent Gbagbo in the western town of Duekoue.
Mr Oueremi was detained in a village close to a national park, where he had been based for more than 20 years.
Some reports suggest the militia leader turned himself in.
It was not immediately clear if he had been been charged with a crime.
Human rights groups had criticised the new government's failure to arrest Mr Oueremi, saying that it showed it was not pursuing justice against both sides in the conflict, BBC Africa editor Richard Hamilton reports.
In its September 2011 report on the post-election violence, Human Rights Watch said Mr Oueremi and his men "were identified by multiple witnesses as among the main perpetrators of the March 29 Duekoue massacre".
Months afterwards UN peacekeepers collected arms from "nearly 90 members" of his group, it added.
Around 3,000 people were killed in Ivory Coast after Laurent Gbagbo refused to acknowledge that his rival, Alassane Ouattara, had won a presidential run-off.
Amade Oueremi's militia backed Mr Ouattara in the conflict.
Mr Gbagbo is currently awaiting trial at the International Criminal Court, accused of crimes against humanity.
A military commander, who insisted on anonymity because he was not authorised to discuss the operation, told Reuters news agency Mr Oueremi had turned himself amid signs the military was preparing for an operation to remove him from the national park.
Denis Badouon, deputy mayor of Duekoue, said the militia leader had been taken into custody on Saturday morning in the village of Bagohouo, near Mount Peko.
According to a UN report from May 2011 Mr Oueremi began supporting anti-Gbagbo rebels as early as 2000 and his men had been hoarding weapons and ammunition since then.
The UN report noted that Mr Oueremi was widely believed to possess "mystical powers".
In photos taken during the crisis, his shirts are pulled tightly over a collection of charms and pendants seen bulging underneath, believed to give him protection from enemy fire, Reuters notes.
The authorities in Ivory Coast have arrested a militia leader suspected of a role in one of the worst massacres during 2011 post-election violence.