Singapore air traffic control was informed by Jakarta when the pilot of Indonesia AirAsia Flight QZ8501 requested approval to take the plane up to 38,000 feet.
Responding to queries from The Straits Times, a spokesman for the Civil Aviation Authority of Singapore said that the communication was part of standard protocol.
"As the Singapore Flight Information Region was QZ8501's onward destination, Jakarta air traffic control informed Singapore air traffic control of the change in altitude as part of normal procedure," said the spokesman.
Singapore air traffic control "immediately acknowledged the receipt of information", she added.
The exchange comprising Jakarta's communication to Singapore and Singapore's response took seven seconds, from 7:17.06 to 7:17.13 Singapore time on Sunday morning, she added.
The Jakarta Post had earlier reported that the communication lasted two to three minutes.
The director of air navigation operator AirNav Indonesia, Mr Wisnu Darjono, was quoted as saying that the aircraft had requested permission from Soekarno-Hatta Airport's air traffic control to turn left at 6.12am local time - an hour behind Singapore time - to avoid a storm.
The pilot of the Airbus 320 aircraft, which was flying from Surabaya to Singapore with 162 passengers and crew members, then requested to take the plane higher to 38,000 feet from its position at 32,000 feet.
"Request to higher level," said the pilot, according to Mr Wisnu, to which the air traffic control- ler replied: "Intended to what level?"
The pilot stated that he intended to rise to 38,000 feet, but did not explain why he wished to fly higher.
Jakarta's air traffic control then contacted Singapore air traffic control.
Mr Wisnu was quoted as saying: "It took us around two to three minutes to communicate with Singapore.
"We agreed to allow the plane to increase its height but only to 34,000 feet, because at that time (another) AirAsia flight... was flying at 38,000 feet.
"But when we informed the pilot of the approval at 6.14am, we received no reply."
The Straits Times understands that the aircraft was about 35 minutes away from Singapore airspace.