Sources said health minister Satyendra Jain had issued a note a week ago to the Public Works Department asking it to get the house vacated.
A senior government official said that as Mishra was no longer a Cabinet minister, he was not entitled to such an accommodation.
Mishra was sacked as the city water minister on May 6 over alleged poor water management.
"After being discharged from his duty as a minister, he could have retained the government's bungalow for 15 days. As per rules, he is no longer entitled to a government bungalow. In view of this, the department has asked Mishra to vacate the accommodation at the earliest," a senior official said.
Sources said PWD Minister Satyendra Jain had issued a note a week ago to the department asking it to get the house vacated at the earliest.
Since he was sacked, Mishra has been continuing with his salvo against Aam Aadmi Party's top leadership, including Chief Minister Arvind Kejriwal.
The Karawal Nagar MLA had earlier accused Kejriwal of accepting Rs 2 crore from Jain and filed a complaint in this regard with the Anti-Corruption Branch (ACB).
After he made the stunning allegation, Mishra was suspended from AAP's primary membership.