The money will be deposited with the Central Pollution Control Board (CPCB).
A bench of justices Ashok Bhushan and K.M. Joseph also directed the state to hand over the illegally extracted coal to Coal India Ltd.
Coal India Ltd will auction the illegally extracted coal and deposit the money earned with the state government.
However, the bench allowed continuation of mining on privately and community owned land subject to permission from the concerned authorities.
The National Green Tribunal (NGT) had fined the Meghalaya government on January 4 after taking note of a three-member committee’s report which stated that there were around 24,000 mines in Meghalaya and a majority of them were illegal.
Earlier the top court banned the transportation of coal in the wake of a coal mine tragedy in the state in December last year.