Indonesia has suspended the AirAsia service on the route yesterday, saying its Sunday flights were not in the contract.
Replying to media queries today, the Civil Aviation Authority of Singapore (CAAS) and the Changi Airport Group (CAG) said in a statement: "An airline can launch a service between two points, but it needs to obtain approval of its flight schedules from the respective civil aviation authorities at each end of its flight routing separately.
It said that on Singapore's end, Indonesia AirAsia had applied to operate a daily flight between Surabaya and Singapore for the Northern Winter Season from October 26, 2014 to March 28, 2015.
"These daily flights were approved as the air traffic rights were available under the bilateral ASA and the slots at the Changi Airport were also available," Singapore's Channel News Asia cited the statement.
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Indonesia's transport ministry has said that the AirAsia plane that crashed last weekend was flying on an unauthorised schedule.
"It violated the route permit given, the schedule given, that's the problem," director-general of air transport Djoko Murjatmodjo said. He added that AirAsia's permit for the route has been frozen until investigations are completed.
Indonesian authorities are also investigating the possibility that the pilot, Captain Irianto, did not ask for a weather report from the meteorological agency at the time of takeoff. Pilots were required to do so before flying, media reports said.
Till now 30 bodies have been retrieved from the Java Sea.
However, continuing bad weather has held back efforts to hunt for the plane's data recorders.