The court also granted Gupta protection from arrest in connection cases registered against him.
A bench headed by Justice Arun Mishra told the government that the stay granted through interim orders on investigations in two FIRs against the officer will continue.
However, the apex court did not pass any direction in connection with the quashing of the FIRs.
Gupta is an accused in the civil supplies scam unearthed in 2015. The other case is connection with the Foreign Currency Regulation Act (FCRA) violations by a Trust established by his father.
The next date of hearing in the case is scheduled on November 4.
Counsels for the state and Chief Minister Bhupesh Baghel contested Gupta's plea, and informed the apex court that a similar petition is pending in the High Court. The state government contended that the High Court had asked Gupta to assist in investigations, while, instead, he had moved an application in the Supreme Court.
Representing the police officer, senior advocate Mahesh Jethmalani alleged vindictiveness of the government in proceeding against Gupta. Jethmalani said these were false cases, while the government is tapping phones of his family members, including of two daughters. He told the court the state government had withdrawn Gupta's promotion.
In September, the top court had asked the government and the Chief Minister to respond to Gupta's plea to transfer cases to the CBI, as he suspected bias.
Special DGP Mukesh Gupta along with other senior police officers was suspended after the Economic Offences Wing lodged cases in the civil supplies scam in the state, alleging criminal conspiracy and illegal phone tapping in 2015.
A 12-member SIT to probe the multi-crore scam, which appears to have had political connections, was constituted by the Congress government after it came to light during the previous BJP regime.
( With inputs from IANS )