Scores of Muslims burnt copies of The Times of India in Patna on Monday, protesting against the reproduction of images of Prophet Mohammad that had first appeared in a Danish publication in September 2005.
The protestors shouted slogans against the newspaper and demanded the editor's dismissal.
Traffic was disrupted in the city's busy Ashok Rajpath area.
The Patna edition of the Times of India published the images on Friday. On Saturday, hundreds of Muslims marched in protest, burnt copies of the newspaper and submitted a memorandum of protest to the editor who is in charge of the edition.
Raj Kumar, the resident editor, told rediff.com that the newspaper published an apology on the front page on Sunday.
He said the newspaper's intention was not to hurt Muslims, but to show how blasphemous the images were.
"But we have realised that it was a mistake on our part to republish it," he said.
The images have sparked protests across the Muslim world. The Danish embassies in Damascus, Syria, and Beirut, Lebanon, have been attacked and burnt by angry protestors.
Life in the Kashmir valley was paralysed on Monday by a general strike called to protest against the decision by some European newspapers to publish images of the Prophet.
Islam prohibits paintings, pictures or any images of the Prophet.