Fernandes, who also owns the London-based football team Queens Park Rangers, tweeted that he was travelling to Indonesia, saying: "On my way to Surabaya where most of the passangers (sic) are from as with my Indonesian management. Providing information as we get it."
Fernandes also tweeted: "My only thought are with the passengers and my crew. We put our hope in the SAR operation and thank the Indonesian, Singapore and Malaysian governments."
Fernandes, along with a large number of Twitter users, has changed his profile picture to the AirAsia badge, with a sombre grey background rather than the usual vibrate red.
The chief executive had been tweeting about the airline's fundraising efforts for the flood appeal, after 160,000 Malaysians were left homeless by heavy flooding in the eastern coastal region of the country.
The chief executive of AirAsia had previously proudly tweeted photos of aid being placed in the hull of an AirAsia plane, in preparation for transporting supplies to the flood victims.
News of Fernandes imminent arrival at Surabaya comes as Indonesia's Metro TV reported that an attempted search operation is currently underway, focussing on waters near southern Borneo.
The rescue operation has been severely hampered by bad weather, with poor visibilitiy preventing any real search operation.
Singapore Civil Aviation Authority confirmed that Indonesia accepted Singapore's offer of assistance at 2:30pm (7.30am GMT).
Singapore's navy and air force are assisting with the search, with the assistance of the Singapore Rescue Coordination Centre.
Airbus have released a statement, confirming that "an A320-200 operated by AirAsia Indonesia lost contact with air traffic control this morning".
The statement reveals the plane's manufacturer serial number, registration and confirmed the plane was acquired in October 2008, and was new when purchased. It had recorded approximately 23,000 flight hours in around 13,600 flights.