Bhagat, who sold the rights of his book to producer Vidhu Vinod Chopra, sparked off a row after he posted a message on his Twitter account on Saturday accusing the '3 Idiots' team of "negating his contribution."
"They (film makers) added a story credit right upfront, without my name, negating my contribution. That is the issue," Bhagat wrote.
The allegations followed a blog post in which he accused the makers of '3 Idiots' of "copying an original story and claiming it to be different."
The team of '3 Idiots' responded by accusing the best-selling author of "lying".
"Bhagat has signed a contract with us, giving us the right to modify or change the story. The contract also clearly states that credit shall be given to him in the rolling credits of the film, which was duly done," director Rajkumar Hirani said.
Bhagat was paid an amount of Rs 9.9 lakhs for rights of the film, according to a document posted on Chopra's website.
Bhagat, who has written four books so far and is one of India's most successful authors, said he was hurt that the credit for the story of the film went to Hirani and co-writer Abhijat Joshi.
Chopra himself landed in controversy at a press conference in New Delhi on Friday after he asked a journalist to "shut up" if he hadn't read the book.
Chopra apologised to the media later, but by then the issue had turned into a mini-storm, with television channels replaying footage of his outburst and social networking sites like Twitter abuzz with comments.
Bollywood has been going through a low-key 2009 and "3 Idiots", which released on December 25, has brought some cheer to the industry. The film grossed over Rs 100 crore in four days and is on its way to becoming one of the biggest hits of last year.
