The services will be along the Thiruvananthapuram-Ernakulam, and Ernakulam-Kozhikode routes.
Police-issued pass is not required for travelling in areas with less than 20% of TPR.
The KSRTC audit report had found serious irregularities in fund management. The report flagged lapses by officials, including the accounts officer.
More long-distance services are set to resume after June 17.
The Karnataka State Road Transport Corporation and its Kerala counterpart were locked in a legal battle over the acronym KSRTC for the past seven years, as both their buses and websites were using it.
The Central Trade Marks Registry announced its final verdict on Wednesday bringing an end to the seven-year-old legal battle between the transport departments of Kerala and Karnataka.
The services began from Thursday night. Three buses are ready to ply from Bengaluru for emergency travel.
After the slump during the lockdown period, the KSRTC made a revenue of Rs 115.26 crore last March. But with the Covid situation worsening, the KSRTC is reeling without even sufficient revenue for meeting the fuel costs.
The action was taken after examining the probe report filed by the Vigilance squad Inspector concerned, the Kerala State Road Transport Corporation said in a release.
In all 1,530 buses of its 3,000-plus fleet would be called back and parked at depots across the state.