Hakeem Al Araibi's case has attracted international criticism because Thai courts have considered Bahrain's request for extradition and asked him to serve 10 years in prison in connection with the 2011 Arab Spring Uprising. He denied the charges.
Arabi was arrested at Bangkok Airport in November when he and his wife came to Australia for their honeymoon.
The 25-year-old said he faced torture in Bahrain and wanted to return to Australia, where he has lived since 2014 and played for Melbourne Football Club.
Thai Foreign Ministry described the case Wednesday as "involving two countries competing for Mr. Hakim's custody rights".
After the Australian police station dealing with Interpol notified the Thai authorities that Araibi had boarded a flight to Bangkok and was the subject of a "Red Notice" launched by Bahrain, Thailand called it "Thai Participation".
"It will take several days before Mr. Hakim arrives, and the Australian authorities informed us that the red notice has been cancelled," the statement said.
"By that time, Thailand's legal proceedings concerning Mr. Hakim had begun and could not be revoked," it said.
A spokesman for the Attorney-General's Office said Araibi could be jailed in August because it would take two to three months for the court to hear his case before a verdict could be reached after the next hearing, scheduled for the end of April.
"So from now on, Hakim must be detained until August at least," Trumph Jalichandra said at a news conference, adding that if Bahrain withdraws his request, he can only be released as soon as possible.
The Australian Office of Civil Affairs confirmed in December that the Federal Police had provided a red notice to the Thai authorities that people were on their way to Thailand, but did not say whether it knew Araibi had refugee status.
The Bahrain Embassy in Bangkok called Araibi a fugitive who should be repatriated.
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