Mohammed Bukhari, 66, said immigration officials have been unable to explain why his name was put in a government blacklist of suspected terrorists.
Bukhari said he found out there was a hold departure order on him when he was stopped at Ninoy Aquino International Airport in January and has not been able to leave the country since.
In a statement yesterday, the Saudi embassy said Bukhari has no ties with terrorists.
"The embassy certifies that Captain Bukhari is known to have a good moral character and is also an honorable man," said an embassy spokesman, who refused to be identified.
The embassy has brought the former Saudia Airlines pilots case before the Department of Foreign Affairs but that was all it could do. "We are just a diplomatic mission and cannot interfere in the operations of a host country," the spokesman said.
Saying that he was being "persecuted, not prosecuted," Bukhari has challenged immigration authorities to file criminal charges against him.
"I will be very happy if they can start investigating me now and then file charges against me in court. It has been six months since they called me a terrorist," he said. "They should charge me now, and if they cannot do that, they should clear my name and set me free."
Bukhari has sued Immigration Commissioner Andrea Domingo and airport immigration chief Simeon Vallada, who recommended Bukharis inclusion in the blacklist.
An immigration bureau source said Bukhari could have been removed from the list had he went to the bureau for interview in February to clear his name but he did not.
In a letter dated February 20, a copy of which was obtained by The STAR, Domingo told Bukharis lawyer, Renato Peralta, to tell his client to show up for the interview.
The interview was "necessary to determine whether or not your client is the same person as the subject of the governments (hold departure) request."
Bukhari was reportedly informed by immigration authorities that his name was included in the blacklist because of an anonymous letter sent to the US embassy in Manila accusing him of "being a supporter of Islamic extremists."
"But that is immaterial now. I think Commissioner Domingo has already acted on his case and has ordered the lifting of any restraint against his departure," the source said, speaking on condition of anonymity.
However, the source also said the bureau may also have been at fault.
"Actually he should have been removed from the watchlist long ago. As I understand it, watchlists have an expiry period and since there was no case against him, he should have been able to leave long ago," the source said.
Bukhari suspects the letter was sent by a group of former business suppliers whom he had earlier sued before a Marikina court for alleged fraud after a deal went sour.
One of those he sued even phoned his house and warned that he would "report to the US embassy that I am a member of al-Qaeda and a terrorist or supporter of the organization" if he did not drop the case, Bukhari said.
Bukharis wife, Amna Bushnag, insisted that her husband had no ties with terrorists.
"My husband went to the Philippines on business all the time," she told Arab News, an English newspaper in Jeddah. "He never had any problems and was never arrested anywhere. He worked for Saudia for almost 30 years and he is admired by everybody."
STAR sources said Bukharis case recently caught the attention of several Saudi newspapers in Saudi Arabia and has been getting front-page treatment.
Amna, who lives in Jeddah, has appealed to Philippine authorities to allow her husband to come home so he could attend the wedding of his youngest daughter next month.
"We wanted to postpone the wedding, but my husband insisted that the wedding should go ahead whether he is able to make it or not," she said. "Hes adamant that it should be as big a wedding as her older sisters."
Bukhari said immigration officials did not arrest him when he was stopped at the airport on Jan. 8. He was questioned for 30 minutes and told to report to the bureaus main Manila office to "clear" his name.
"I am not a terrorist. I am a victim of prejudice in the Philippines. You can only accuse a person for what he has done and not for what he is. My problem is I am a Saudi, an Arab, a Muslim and a pilot. Therefore, I am a terrorist," he told The STAR in an earlier interview. With Jose Aravilla