"We believe he is not likely to be a member of any terror group and we believe he was trying to migrate to Germany," said Malaysia's national police chief Khalid Abu Bakar.
Khalid said authorities had not yet identified the other man.
Malaysian Airlines flight MH370 disappeared early Saturday with 239 people aboard, sparking an international search for the plane in waters off Southeast Asia.
Revelations that two passengers on board were travelling on EU passports that were stolen in Thailand had fuelled speculation of a terrorist attack.
Khalid identified the man as Pouria Nour Mohammad Mehrdad. He said the 19-year-old boarded the plane on an Austrian passport whose owner had previously reported it stolen.
Asked why police believed the man was seeking to emigrate to Germany, Khalid said authorities had been in contact with his mother, who was waiting for him to reach Frankfurt, but he gave no further details.
However, he said police were still considering all possibilities in terms of criminal involvement in the plane's disappearance, when asked whether police thought the revelation made them consider terrorism less likely in the case.
"At this moment, I would not say less likely. Same weightage to all until we finish our investigations," Khalid said.