Jaybe Ofracio, 31, was arrested by Northern Ireland authorities last Friday and charged with "two counts of making funds available to others for the purpose of terrorism," a report from the Philippine Embassy in London said.
Ofracio did not enter any plea during his arraignment on Wednesday at the Belfast Crown Court. He was ordered held without bail until his next court appearance on Feb. 11.
His wife, Indira Abdullah, a nurse at the Royal Victoria Hospital in Belfast, was also brought in for questioning but later released.
The couple hail from Cotabato and have three children with them in Belfast. Ofracio reportedly holds two jobs, one as a cleaner at a hardware store and the other as a cashier at a university.
Detective Inspector Mark Brown testified that the charges concerned support for the JI, a militant group that seeks to create a pan-Islamic state encompassing Indonesia, Malaysia and the southern Philippines.
The United States and Australia have accused the group of forging ties with Osama bin Ladens al-Qaeda network and conducting several bombings in Indonesia, including the October 2002 Bali nightclub blasts that killed 202 people.
Brown said police had seized telephone and financial records as part of their investigation, which focused on an e-mail sent from Malaysia.
"We conducted a number of searches in Belfast and a number of searches in the Philippines and we are looking to connect them," Brown said.
Ofracios defense lawyer, Catherine McGinley, said her client "has given a full and frank account of how he became an associate with a person who is detained in Southeast Asia." She offered no details.
Government documents showed that Manila, the US and Australian intelligence authorities provided information that led to the arrest.
Authorities have also searched the couples home in southern Cotabato City, but it wasnt clear if anything was found there.
President Arroyo ordered the DFA yesterday to protect the rights of the accused.
In an interview over Radyo Bombo yesterday, Mrs. Arroyo said Ofracios rights will be protected. She, however, reiterated the governments policy not to condone any acts of terrorism.
"This is a serious case involving terrorism and our nationals should prove their innocence or face the full force of the law," the President said.
Meanwhile, acting Foreign Affairs Secretary Sonia Brady said Ofracio is being provided with adequate legal representation through the Philippine consulate in London and the honorary consul in Belfast.
Brady said she hopes that "other governments will continue to trust the Philippines" particularly in its involvement with the fight against terrorism.
She disclosed that she is not aware of the Philippine government providing information to Northern Ireland authorities, at least not on the part of the DFA. But she admitted that there have been several cases in the past where various government agencies communicate directly with their counterparts, particularly in the field of law enforcement.
"Government lines of communication are clearly established. These are just incidents which affirm that we cooperate with each other in resolving this problem," Brady said. With reports from AFP, Marichu Villanueva