Police had filed a petition before the Judicial Magistrate V Jayakumar at Melur, near here, seeking issue of NBW against Dayanidhi, for whom a special police team was on the lookout.
Dayanidhi and nine others are facing charges that companies owned by them had mined sand and granite without permission.
Dayanidhi had earlier opposed the police plea for the arrest warrant against him, saying he had filed an anticipatory bail plea in the Madras High Court "in view of the changed situation in the case".
He had stated that arrest warrant could not be issued by courts solely for production of accused before the police in aid of investigation, and what could not be done directly, could not be done indirectly (through court).
He also stated that he was being politically victimised as he was the son of Central Cabinet Minister and grand son of the DMK president M Karunanihdi.
On a complaint from the local village administrative officer, police had charged Dayanidhi and Nagarajan, partners in Olympus Granites Pvt Ltd, with encroaching on the adjacent government land and taking away large quantity of granite illegally without quarrying in the permitted area and causing loss of Rs 44 crore to the Government by illegal quarrying.
Cases had been registered under various IPC sections including 120(b) (criminal conspiracy), 447 (criminal trespass) and 420 (cheating) against them.
Government cracked down on the firms after former Madurai Collector U Sahayam in a report, estimated the losses incurred from illegal granite mining at around Rs 16,000 crore.
Police had alerted immigration authorities to help them in preventing Dayanidhi and other accused from leaving the country. The companies' accounts had already been frozen.
