The action of environment ministry comes close on the heels of growing public outcry over the illegalities in the mining sector, as clearly indicated in the commission report.
Headed by retired judge MB Shah, the commission says the scam in Goa is worth nearly Rs 35,000 crore and that there is proof of "serious illegalities and irregularities."
Earlier, Goa government on Monday suspended the operation of all existing mining leases with effect from Tuesday.
"This was done to scrutinise clearances obtained by the leaseholders and not to allow continuation of operations without verification of requisite approvals in the coming mining season," said sources.
The State Mines and Geology Department issued this notification directing the mines to stop their operations.
Sources at state Goa government said that the mines would not be allowed to operate, if they were found to be carrying out work without the necessary permissions.
The mines have been asked to submit their documents before they could start operations.
The notification states that the mine owners need to submit all the documents including permissions from the Union Ministry of Environment and Forest.