Speaking in Indonesia's second-biggest city of Surabaya after meeting with distraught relatives of some of the 162 passengers, Fernandes said he "apologised profusely" for the accident.
"The passengers were on my aircraft and I have to take responsibility for that," he said, adding that he was focusing on supporting the families.
Aerial searchers spotted debris in the Java Sea that officials confirmed was from the plane that had been travelling from Surabaya to Singapore. Three bodies were then recovered.
An earlier statement from his company said employees of affiliate AirAsia Indonesia, which operated the crashed plane, had been sent to the site where debris was found and would fully cooperate in the investigation.
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"There is at least some closure as opposed to not knowing what's happened and holding out hope," Fernandes told reporters.
He said the pilot of the ill-fated plane was "extremely experienced" with 20,000 hours of flying.
"There were some very unique weather conditions and let's wait for the investigation to be concluded."
The accident was the third disaster this year involving a Malaysian-owned carrier.