Vigilance and Anti-Corruption officials also conducted raids at 34 places, including in Chennai and Salem, as part of the probe, A Vigilance release here said.
Former District Collectors of Madurai M Mathivanan and C Kamaraj were booked under different sections of IPC and Prevention of Corruption Act, the release said, charging them with "wilfully suppressing facts" regarding the irregularities.
Former Madurai Collector U Sahayam in a report to the government had pegged the alleged losses incurred from illegal granite quarrying to the tune of around Rs 16,000 crore.
Granite magnate P R Palanisamy and scores of government officials have been booked in connection with the alleged scam.