The notification was issued on Monday by the state Urban Development department.
The state had decided in 2006 to regularise these structures under a special law after the Bombay high court ordered their demolition.
In 2006, the state appointed the Thane collector as designated authority to regularise the buildings, but due to heavy workload, the collector had regularised around 50 buildings out of 95 that had applied for regularisation.
MLA Jyoti Kalani said the order will bring relief to lakhs of residents. The collector, due to his busy schedule, took long to regularise the structures.