Mohammad Omar Al-Bokhari spent the night at the Philippine National Police headquarters where he was brought after immigration officials held him at the Manila airport before he was to fly out to Riyadh on Friday.
National Security Adviser Roilo Golez told The Associated Press that Bokhari was put under "character verification custody" as part of a Philippine investigation "in close collaboration with US authorities."
"We gave the clearance to the police to have him released," Golez said, adding that the decision was made by a Cabinet group in charge of national security.
"We just wanted to be sure," Golez said. "There was assurance from the government of Saudi Arabia and Saudia Air."
Philippine officials believed Bokhari might be a brother of Adnan Bukhari, 41, who has been questioned about the US attacks and is a student at Flightsafety International in Florida, which trains commercial jet crews.
An apparent relative, Ameer Bukhari, was a student pilot there when he was killed in a mid-air collision exactly a year before Tuesday’s attack, and Philippine officials said they believed Al-Bokhari attended the same school.
"I have no brother over there," Bokhari said as he was led away by immigration officers and police in black uniforms and submachineguns.
"He is not related" to Bukhari, Golez said. "We just wanted to be sure. ... We continue doing these verification checks. We cannot be over-careful here."
"He understands that these are very difficult times," Golez said.
Senior Superintendent Jaime Caringal, PNP-Intelligence Group deputy chief, said Bokhari was turned over to the custody of Immigration Commissioner Andrea Domingo, who in turn handed over the pilot to the Saudi embassy authorities for his flight home.
"Bokhari came out very consistent with all his responses and answers to our intensive questioning," Caringal said.
A ranking official of the Saudi embassy and the manager of Saudia Airlines, who rushed to Camp Crame Friday night, vouched for the pilot.
Domingo said Philippine authorities became suspicious after they learned Bokhari was a last-minute substitution in the crew for Flight SV862 from Jeddah, Saudi Arabia, to Manila on Thursday.
He had been scheduled to fly to Riyadh on Friday afternoon, but the flight left without him as he was questioned and fingerprinted at Manila’s international airport.
There was no immediate word on when Bokhari was to leave Manila. – Jaime Laude