The government would be forced to confiscate the plots if the company didn't pay royalty to the government for the soil used.
A company spokesman declined to comment on the development.
Navi Mumbai SEZ was first served a notice on January 8 by the tehsildar's office to stop land filling and pay royalty for the soil used. The company was given seven days to pay royalty and fine as per the Land Revenue Code 1966.
Fresh notices were served on February 5 and 13 for stopping the "illegal land filling activity" and payment of royalty of Rs 4.58 crore (Rs 45.8 million). The company neither responded to these notices nor paid royalty.
"We have confiscated bulldozers, excavators and other machinery from the site," said Kedare.