He faces three counts of negligence and one of "deliberately" destroying or damaging an aircraft causing death.
Following the reading of the charges against him, the trial was adjourned until August 4, when Komar's defence will have a chance to answer the charges.
The Yogyakarta crash killed 21 people and injured 112 people.
Sixteen of the dead were Indonesian nationals, while the remaining five were Australians following a government minister who was on an official visit to Indonesia.
A government investigation into the crash concluded that Komar was approaching the runway at almost double the landing speed and ignored automatic warnings and pleas from his co-pilot to circle around again.
The investigation also found that Komar, whose license was revoked after the crash, ignored 15 warnings from the control tower to abort the landing.
|Pilots say the trial will only criminalise them and not improve aviation safety [EPA]
But his arrest led to protests from his colleagues. The Indonesian pilots' association has argued that the trial would only criminalise pilots and not improve aviation safety in the country.
The association says that under international aviation regulations police are not allowed to use information from the aircraft's "black box" flight recorder to launch a criminal prosecution of the pilot.
Komar's lawyer said it was "impossible" that his client would have caused the crash deliberately.
"We will at the very least question why the pilot is being criminalised for an accident. This has not yet happened anywhere in Indonesia or in the world," Muhammad Assegaf told AFP.
"Punishing the pilot would give rise to fears among pilots that one day they could be treated as a criminal over an aircraft accident."
The Yogyakarta crash was among a string of deadly air accidents across Indonesia that prompted a government audit to evaluate safety in an industry that has seen explosive growth since liberalisation in 1999.
Of 54 airlines audited, none made it to the top safety category and six were given a three month deadline to improve safety standards or face closure.
But Chappy Hakim, who led the team that recommended that the government improve inspections, enforce sanctions and change the industry’s management, says hardly any action has been taken.
"I'm disappointed because more should have been done. If they would have been brave enough to take strong actions much more could have been done. The situation worries me," the former air force chief told Al Jazeera.
Jusman Safei, Indonesia's transport minister, rejected claims that not enough strong action had been taken, saying that much had been done to improve inspections and the quality of aircraft.