Bahrain's Ministry of Foreign Affairs said Sunday Araibi had fled the country while awaiting trial on charges of arson, and that issuing an worldwide warrant for his arrest is "standard practice".
Al-Araibi has said he believes he was targeted for arrest because of his Shiite faith and because his brother was politically active in Bahrain, a country that has a Shiite majority population but is ruled by a Sunni monarch.
"It took several days after the arrival of Mr Hakeem before the Australian authorities informed us that the red notice had been cancelled", the statement said.
"The Thai government should see that Bahrain's sole motive is to further punish Hakeem for the peaceful political opinions he expressed", Amnesty International Thailand campaigner Katherine Gerson said in a statement.
But they were detained immediately when they landed at Bangkok's Airport in response to an Interpol "red notice".
After being sentenced by Bahrain to 10 years' jail in absentia, al-Araibi fled in 2014 and was later granted refugee status by Australia and lives in Melbourne. "I have done nothing wrong in Bahrain but if I go back I will be tortured again and I will be sentenced to 12 years in jail".
On Monday, he urged a court in Bangkok not to extradite him to his home country.
The ministry said it had not been aware of al-Araibi's case and would not have become involved had it not received the red notice alert and Bahrain's subsequent arrest and extradition request.
"The Bahraini government knew that he would be arriving in Thailand so they coordinated with Thailand's permanent secretary of foreign affairs to detain him, pending documents sent from Bahrain", Surachet told BBC Thai.
Prime Minister Prayut Chan-o-cha said the case would be tried in court in compliance with Thai judicial procedures and the government is not in a position to interfere. Australian Prime Minister Scott Morrison has also spoken out strongly on behalf of Al-Araibi's freedom.
"I would be very disappointed if as a result of how this was handled that that relationship between the Thai and Australian people were affected", he told reporters in Melbourne on Wednesday.
The letter said Al-Araibi had been prosecuted as a result of an allegation related to his "opposition to or criticism of the Bahraini government and his other alleged offences also constitute political character".
The court hearing the case will need two to three months to give its ruling after the next hearing in late April, said a spokesman for the attorney general's office on Wednesday.
"So between now and then, Hakeem will have to be in custody for at least until August", Trumph Jalichandra said, adding that he could only be released sooner if Bahrain withdrew its request.
"If you look at the number of foreign defendants, they pay their bail and jump bail and then don't show up in court", Chatchom Akapin, the office's director general for worldwide affairs, said, adding that the policy applied "not only to Hakeem".
He said Federation Internationale de Football Association has not discussed imposing sanctions on either Bahrain or Thailand over the case.
Plans had been made by FFA a year ago to play a friendly match against China in Bangkok as part of the team's preparations for the AFC Under-23 Championship qualifiers to be held in Cambodia in March, but alternatives are now being sought.