The two teams led by additional SPs Manoj Jha and Pramod Sanger started the investigation on Wednesday.
They visited the affected villages and recorded the statements, she said.
Police has registered 106 cases including 43 murder cases in connection with the riots. 408 people from the violence hit Muzaffarnagar have been named in the cases, she said.
The UP government had formed SIC earlier this week to investigate the cases registered in connection with the riots.
While Saxena will be heading the investigations in Muzaffarnagar, IGP (Crime) Ashish Gupta was yesterday made the officer in-charge to supervise the overall probe at the state police headquarters in Lucknow.
Communal clashes in Muzaffarnagar and its adjoining areas claimed 49 lives and left thousands of others homeless.