Issuing notice to chief secretaries of all states, the tribunal said large-scale mining activity was carried out in violation of laws, causing losses to state revenues to the tune of lakhs of crores of rupees.
The five-member bench headed by tribunal chairperson Justice Swatanter Kumar asked the states to respond by Aug 14.
The bench said the contention is that majority of those carrying out activity of removing minerals from the river bed have no license to extract sand.
"In the meantime, we restrain any person, company, authority to carry out any mining activity or removal of sand, from river beds anywhere in the country without obtaining environmental clearance from environment ministry and license from the competent authorities," the order said.
Nagpal, a 28-year-old 2009 batch officer of the Indian Administrative Service, who had taken on the sand mafia in Noida, was suspended by the Uttar Pradesh government July 29.
The state government suspended Nagpal accusing her of jeopardising communal harmony by ordering demolition of a wall of a mosque. She has denied the charge.
The green tribunal said removal of minerals from riverbeds was posing threat to their flow, forests on riverbanks and most seriously to the environment of these areas.
Citing a Supreme Court order, the bench said: "Anyone carrying mining activity in less than five hectares, are expected to take environmental clearance."
"Besides, sand mining on either side of the rivers ... is one of the causes for environmental degradation and also a threat to the biodiversity," it said.
The bench directed the deputy commissioners, superintendents of police and mining authorities of all states to ensure compliance of the order.