A senior advocate, who is assisting the tribunal as an amicus curiae in the mining matter, said a report of a high-level committee was submitted on January 2 before a bench headed by NGT chairperson A K Goel.
The report stated that majority of the mines in the state were operating without a lease or licence.
The NGT imposed Rs 100 crore fine on the state government as a "deterrent" and for its "inaction" to curb illegal mining in the north eastern state.
The lawyer said during the hearing, the state government admitted that a large number of mines were operating illegally.
At least 15 miners are trapped in the 370 foot-deep illegal coal mine in Lumthari village of East Jaintia Hills district of Meghalaya since December 13 and all efforts to pump the water out of flooded mine have been in vain.
The owner of the illegal rat-hole mine Krip Chullet was arrested on the evening of December 14.
The state government has spent roughly over Rs 50 lakh for hiring various utilities to rescue the trapped miners.
On Thursday, the Supreme Court had expressed strong dissatisfaction over the rescue efforts to trace the miners and had asked the state government to bring them out dead or alive.