National Under-23 midfielder Fahmi Daniel Zaaim tested positive for Covid-19 upon arrival in Phnom Penh, Cambodia, on Friday.
The 20-year-old is said to have tested positive after a polymerase chain reaction (PCR) test.
Team coach Brad Maloney said he is saddened by the incident as Fahmi has been one of his core players.
"We had one positive indication which was confirmed with a PCR test, and the medical team had managed it accordingly," said Maloney yesterday.
"Fahmi went immediately from the airport to the medical facility where he remains in isolation at the moment."
According to Cambodia's Covid-19 procedures, patients will continue to take tests until they get a negative result and are without symptoms for at least three days before cleared from quarantine.
Maloney said Fahmi is asymptomatic and hopefully he will be able to play at least one game for Malaysia in the Asean Under-23 Championship from Feb 14-26.
Meanwhile, following Indonesia's withdrawal on Friday due to Covid cases in their team, Group B has been reduced to three teams: Malaysia, Myanmar and Laos.
"It's a real shame Indonesia had to withdraw because we were looking forward to the challenge since plenty of their youngsters had also made their senior team debuts and would have been tournament favourites," said Maloney.
The Malaysian team had their first training session in Cambodia yesterday, after a 24-hour quarantine.