"We believe that he is not likely to be a member of any terrorist group, and we believe he is trying to migrate to Germany," Malaysia's national police chief Khalid Abu Bakar told a press conference.
The young man's mother was waiting for him in Frankfurt, the official said, and when he didn't arrive, she contacted Malaysian authorities.
The 19-year-old Iranian, identified as Pouria Nour Mohammad Mehrdad, boarded the plane using a stolen Austrian passport.
However, he did not rule out terrorism as a possible cause of the disappearance of the plane.
"I would not say (terrorism is) less likely. Same weightage to all until we finish our investigations."
The identity of the other man using stolen passport was still under investigation, Xinhua reported.
The news that two passengers on board were using stolen passports had led to speculation of a terrorist attack.
Referring to the police probe, Khalid said the authorities are mainly looking into four areas: hijacking, sabotage, psychological problems of the passengers and crew and personal problems among the passengers and crew.
Elaborating on the personal problems, the official said there may be passengers on the flight who has bought huge sums of insurance or owed a lot of money.
The fate of the Malaysian Flight MH370 with 239 people on board that vanished about an hour into a flight to Beijing remained a mystery, as a massive multilateral search, now in its fourth day, failed to turn up any trace of the Boeing 777 plane.