The cinemagoers, who were attending an international film festival in the city of Trivandrum in Kerala, were later freed but they face charges of "failure to obey an order issued by a public servant, thereby causing obstruction or annoyance to others".
And at a cinema in Chennai on Sunday, eight people who did not stand for the anthem were assaulted and abused, police said. The eight were later charged with showing disrespect to the anthem.
The arrests and reports of assault follow last month's Supreme Court ruling that the national anthem be played before every film and that audiences stand while it is played - and they make it clear that authorities are taking the ruling seriously.
"If we did not sit on chairs, I thought we would lose the seats," one detainee told the Indian Express.