The occupancy of special trains is being monitored on a regular basis and additional special trains may be run based on the requirement, the national carrier said.
However, all other regular trains and suburban trains run before the lockdown will remain suspended for the time being, it said.
All special trains 12 pairs running on the Rajdhani routes since May 12 and 100 pairs operating since June 1 will continue.
The limited special suburban services which began recently in Mumbai to ferry essential services personnel identified by the local authorities will also continue to run, officials said.
Earlier, the national transporter had suspended all services till August 12.
With the suspension of passenger trains indefinitely, Indian Railways has estimated a loss of around Rs 40,000 crore in its passenger business for this fiscal.
The extension of the suspension comes at a time when active Covid-19 cases in India stand at 639,929, while 15,83,489 people have recovered, according to the Union Health Ministry. On Tuesday, a single day spike of 53,601 Covid-19 cases pushed India's virus caseload to 22,68,675 with the death toll climbing to 45,257.