The BJP-led government was allotting permits to migrants and depriving the "sons of the soil" of new permits, the Raj Thackeray-led Maharashtra Navnirman Sena said in a statement.
Shalini Thackeray also met Regional Transport Officer M B Jadhav and demanded modification of rules so that Marathis get preference, it said.
The state government's directive that the person seeking auto license must be domiciled in Maharashtra, know Marathi, and must not have a criminal record was not being implemented properly, the party alleged.
She also said that only 5 per cent of the permits went to women, which was too little. The party also opposed the hike in permit fee, the statement said.
Claiming that 70 per cent of new autorickshaw permits were given to non-Marathis, MNS chief Raj Thackeray had threatened on Wednesday that his partymen would set on fire such autos if they were seen plying on roads.