Sathasivam was not allowed on an Air India flight from Kochi to Thiruvananthapuram on Tuesday night when he arrived minutes before take-off.
The governor reached the tarmac at 11.28 pm, minutes before its departure, but the ladder was pulled up and the plane prepped for take-off.
Sathasivam's aides claim that he was delayed by official programmes.
They say that a governor has to be the last person to board a flight, so there may have been some "miscommunication".
Sathasivam was chief justice of India for a year till April 2014. Four months later, he became the governor of Kerala.
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