The official spokesman tweeted that PMO has asked "Ministry of Civil Aviation for a report on delay in Air India flights on account of VIP travels in the recent past".
The Civil Aviation Ministry, in turn, has sought a report from Air India on the two incidents.
"We are awaiting reports on the (two) incidents from Air India," Civil Aviation Secretary R N Choubey said, adding it would take a call on the matter after receiving the reports.
The development came after reports surfaced about inconvenience caused to passengers of two flights of Air India since June 24 because of Rijiju and Fadnavis.
A media report surfaced on Wednesday that on June 24, three members of a family, including a child, were offloaded from Leh-Delhi Air India flight at Leh to accommodate Rijiju along with Jammu and Kashmir Deputy Chief Minister Nirmal Singh and an aide. This also led to some delay in the flight.
Rijiju had claimed it was not a "delay" as the departure of the flight was advanced due to technical reasons.
Another report a few days back said that an Air India flight to Newark from Mumbai was delayed by nearly an hour on June 29 after it was reported that an aide of Fadnavis travelling with him had not carried his passport with valid US visa.
Principal Secretary Pravin Pardeshi was cleared at the check-in but was held back before boarding as the passport he was carrying did not have the valid visa.