He said that, based on radar and satellite readings, he thought it most likely that the Adam Air Boeing 737 had fallen into the sea.
The aircraft disappeared on Monday during stormy weather over Sulawesi island in the northeast of Indonesia
On Tuesday morning, aviation officials, the Indonesian military and police reported that 90 bodies were scattered at the crash site, and that a dozen people might have survived.
Later, however, Hatta Radjasa, the country's transport minister, said those statements were based on rumours from villagers passed on to local officials, adding that "search and rescue team is still looking for the location".
Search and rescue
Rescue and search teams hiked through heavy rain and slippery forest paths on Tuesday in search of the jetliner.
The aircraft sent distress signals halfway through its two-hour flight from Indonesia's main island of Java to Sulawesi.
More than half of the flight path was over the Java Sea, the Maluku Sea and other smaller waters, but most of the focus was over land.
The search was called off on Tuesday due to bad light.
Tuesday's apocryphal descriptions of the crash site were vivid, with officials saying 90 corpses and debris from the plane were scattered over a 300-metre area of forests and jagged cliffs.
"Everything was in order, the condition of the plane was good"
Ichsan Tatang, national aviation chief
The report suggested that a dozen people may have survived, bringing anguish and hope to waiting relatives.
Referring to a local police chief, the National Search and Rescue Agency's Karnoyudo said: "Once he went to check for himself he found it was not true."
The accident followed weeks of seasonal rains and high winds in Indonesia, which have caused deadly floods, landslides and maritime accidents, including the sinking of a ferry in the Java Sea on Friday, in which more than 400 people died or went missing.
On Tuesday hundreds of people gathered at Manado airport, the aircraft's destination, upset and angry with officials amid conflicting reports of the crash.
Budget travel concerns
Adam Air is one of at least a dozen budget carriers that have emerged in the country since 1999, when the industry was deregulated.
The rapid expansion has led to cheap flights to scores of destinations around the country, but has raised some safety concerns, since maintenance on the leased aircraft is reportedly poor.
Ichsan Tatang, the national aviation chief, said that the aircraft involved was 17 years old, had flown 45,371 hours and passed its last inspection on December 25.