On Monday police questioned Marwoto for the first time since naming him the official suspect in the criminal investigation into the crash.
He could be jailed up to seven years if found guilty on all six counts of manslaughter.
In the March 7 incident, the Boeing 737-400 jetliner carrying 140 people skidded off the runway and ploughed into a rice field before bursting into flames. Many of the 119 survivors suffered severe burns.
An Indonesian transport safety panel partially blamed the pilot for ignoring the 15 warnings, and for causing the aircraft to destabilise by trying to descend too fast and too steep.
The panel said the pilot's failure to observe safety procedures had contributed to the crash, but refused to conclude if the crash was due to human error or pilot error.
The Aviation Safety Network has recorded 48 air accidents in Indonesia in the last decade, 23 of which resulted in fatalities with more than 700 people killed.
March 7, 2007 (above): Garuda airlines Boeing 737 overhsoots runway at Yogyakarta, Java. 21 die and many others escape burning wreckage.
1 January, 2007: AdamAir Boeing 737 crashes into the sea near Makassar, Sulawesi. 102 passengers and crew presumed dead.
5 September 2005: Mandala Airlines Boeing 737 crashes into residential area shortly after take off at Medan, Sumatra. 101 people on the plane and 44 on the ground killed.
26 September, 1997: Garuda Airbus A300 hits hillside descending into Medan. All 234 passengers and crew killed in Indonesia's worst single air disaster.
Source: Aviation Safety Network
Speaking after the interrogation, Marwoto's lawyer said the legal action sets a bad precedent and may make other pilots reluctant to fly.
Muhamad Assegaff said cases involving air incidents should be heard by aviation specialists, and not in a criminal court.
"Plane accidents should be treated similar to boat accidents which will go to a maritime court," he said. "Marwoto, the Garuda pilot, if necessary can be brought to an aviation court."
Indonesia's aviation safety record has come into question many times over recent years, raising concerns that industry infrastructure and personnel are insufficient to deal with strong growth in air travel across the country.
Some international aviation groups have urged Indonesian authorities to suspend the criminal probe and to focus instead on identifying the underlying reasons for a spate of deadly accidents that have plagued civil aviation.
The crash was the third accident in 2007 involving a commercial jetliner in Indonesia, prompting foreign governments to issue warnings about the country's air safety standards.
Last year, in the wake of the Yogyakarta crash, the European Union announced that it was banning all Indonesian airlines from its airspace.
The ban, which is reviewed every six months, remains in effect.