In his letter Sathasivam pointed that he and his wife were not accommodated in the flight even after boarding pass was issued to them and sought an inquiry into the incident, a Raj Bhavan official said.
He also wanted the Ministry to ensure that such instances do not recur in future.
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Raj Bhavan had described leaving the Governor behind as a "serious mistake" while Air India maintained that the flight left on time as part of its policy of carrying out operations on time.
According to them, the Governor reached Kochi airport at about 11.30 PM as per the advice of a district administration official who was coordinating the travel arrangements there.
As per the advice, the Governor was required to reach the airport before 11.40 pm, but when he reached the airport the flight had already taken off at 11.30 pm
, the sources said.
They also claimed that Air India's ground staff did not communicate with the flight's pilot about the Governor already being at the airport.
The Governor later reached the capital by road.