The Hawker chartered aircraft was taxing and was about to take off when the fuel warning signal was triggered, forcing the pilot to abort the flight.
Naidu was on his way to Jaipur to file his nomination papers for the Rajya Sabha polls.
"Both Naidu and Rudy are safe. They were delayed by about two hours," BJP sources said.
Naidu, along with Rudy, had to take another flight to reach Jaipur for filing his nomination papers.
BJP has nominated Naidu as the party's candidate for Rajya Sabha from Rajasthan, where the party enjoys a majority.
Tomorrow is the last date for filing of nominations for the elections to Rajya Sabha, polling for which will be held on June 11.