However, Raju also said that the incident is "too small" for the Prime Minister's Office to step-in.
"Whatever has happened should not have happened...I need to get to the truth... As Civil Aviation minister I apologise (for the inconvenience caused to the passengers)," Raju told reporters.
He was responding to a volley of questions on the twin incidents involving Minister of State for Home Affairs Kiren Rijiju and Maharashtra Chief Minister Devendra Fadnavis.
The Minister said that the Ministry would submit a report to the PMO, which has sought details on "delay in Air India flights on account of VIP travels in the recent past".
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According to Raju, the incident is "too small" for the PMO to take note of.
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.
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.