The accused, identified as Narayan Mohanty, was nabbed from the busy court square area by sleuths of the state crime branch police, which is investing the case, a crime branch official said.
Mohanty, said to be a petty businessman based in Raikia, was here in connection with some work when the crime branch police apprehended him, they said.
The nun was allegedly raped by a mob in K Nuagaon area on August 25, 2008 during the communal riots, which broke out after the murder of Saraswati and his four disciples at Jalespata ashram during Janmashtami festival on August 23.
Saraswati's murder had triggered large scale violence in Kandhamal and some other places in which at least 38 people were killed and hundreds rendered homeless.
At least 27 people have been arrested in connection with the rape case so far. The last arrest had been made in May when the state crime branch nabbed one Apurba Rout for his alleged involvement in the case.