The BMKG agency said initial analysis suggested icy conditions in the air had caused the engine to stall.
The Airbus A320 vanished with 162 people aboard en route from Surabaya in Indonesia to Singapore on December 28.
The discovery of four large objects believed to be plane debris has raised hopes of finding the fuselage, where most bodies are believed to be trapped.
Just 30 bodies had been recovered from the Java Sea as of January 3.
The plane’s black boxes, its flight data and cockpit voice recorders, have yet to be located.
BMKG found conditions at the time of the plane’s disappearance suggested it had probably flown into a storm.
“From our data it looks like the last location of the plane had very bad weather and it was the biggest factor behind the crash,” said Edvin Aldrian, head of research at BMKG.
“These icy conditions can stall the engines of the plane and freeze and damage the planes machinery.”
Officials have said the plane was travelling at 32,000ft when the pilot’s last communication was a request to climb to 38,000ft to avoid bad weather.
Search chief Bambang Soelistyo said four large objects as well as oil slicks had been detected by sonar.
The biggest object is 59ft long and 18ft wide, he was quoted as saying by the Associated Press news agency, adding he believed the objects were parts of the plane. Another object is said to be 32ft long.
Bambang Soelistyo said an ROV (remotely operated underwater vehicle) was being lowered into the water to get an actual picture of the objects, which were at a depth of 98ft.
But he warned that waves up to 17ft high were hampering the search effort.
A flotilla of ships, including two from the US navy, are converging on the site where the objects were located and preparing to put divers into the water.
A Russian search team, including 22 deep water divers and a remotely operated submersible vessel, is expected to join the hunt for the black boxes after arriving in Pangkalan Bun on January 3.
It has emerged that AirAsia did not have official permission to fly the Surabaya-Singapore route on the day of the crash but was licensed on four other days of the week.
The Indonesian authorities suspended the company’s flights on this route pending an investigation. AirAsia said it would “fully co-operate”.
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