But the pilots were unaware of this because a cockpit alarm did not go off, the report said.
On takeoff, flaps help a plane leave the ground and climb by changing the wing's shape to provide more lift.
The investigators did not say, however, that this caused the crash and offered no hypothesis as to what may have triggered Spain's worst air disaster in 25 years.
Some of the 18 survivors have said the Spanair plane struggled to gain speed and altitude during takeoff. The aircraft crashed tail-first, bounced three times as it skidded through a grassy area near the runway, then largely disintegrated and burned after coming to a halt at the edge of a stream.
The findings were based on data from the MD-82's flight data and cockpit voice recorders and contained in a preliminary report on the Aug. 20 crash.
The report was carried in Spanish media, and Spanair confirmed it had been distributed to the government and the plane's manufacturers. The investigators work for the civil aviation department of Spain's Development Ministry.
The report said McDonnell Douglas recommended after a deadly MD-82 crash in 1987 in Detroit, Michigan, that airlines operating such planes check their take-off warning system before each flight.
The system is supposed to warn pilots if planes trying to get off the ground are not in fact properly configured for takeoff.
But Spanair's policy is to check the system before a plane's first flight of the day and during stopovers, but in the latter case only if an entirely new cockpit crew takes over for the continuing leg, the report said.
If one member of the cockpit crew stays on for this leg, Spanair does not carry out such checks and this was the case of the plane that crashed, the investigators said. The flight originated in Barcelona, stopped off in Madrid and was to go on to Las Palmas in the Canary Islands, and the pilot and co-pilot were not relieved.