Police said the clashes occurred in Godhra town on Wednesday, where 59 Hindus were burnt to death in a train compartment in 2002.
The deaths triggered months of bloody Hindu-Muslim rioting in which nearly 2000 people, mostly Muslims, were killed.
When police entered the predominantly Muslim area of Shatpool on Wednesday to arrest two people accused over the Godhra train carnage, a mob stood in their way, superintendent of police Piyush Patel said.
"As soon as the police reached Shatpool to arrest Salim Panwala and another Godhra accused, a huge crowd of Muslims collected and began pelting (them with) stones."
Police said they fired four warning shots into the air and threw several teargas canisters to control the group.
The Babri mosque was destroyed
by Hindu zealots in 1992
In the mayhem, 12 people were injured and a police sub-inspector and two head constables were also hurt, Patel said.
He added the area was still tense late on Wednesday.
Muslims and Hindus in Gujarat have been at loggerheads since Hindu zealots destroyed the Babri mosque in Ayodhya in 1992.
Hindus say the mosque was built on the birthplace of their deity-king Ram, and India's governing Bharatiya Janata Party have campaigned for a temple to be built in Ayodhya.
However, Muslims want a mosque to be rebuilt on the site.
Although Muslims were initially blamed for the 59 Hindus who were killed in Godhra in 1992, a subsequent investigation found that evidence of Muslim complicity was inconclusive.