Reading a statement at the Pasay court, Dwikarna said: "I am not a terrorist."
"I know nothing about the Jemaah Islamiya or al-Qaeda and their activities," he said, referring to two groups of militants who police allege were plotting to stage terrorist attacks in Southeast Asia.
The Indonesian claimed Philippine authorities had set him up to be arrested for possession of C-4 plastic explosives, which authorities said they seized from his baggage at the Ninoy Aquino International Airport in March.
The court found him guilty on the explosives charge in July. Two Indonesians arrested with him Abdul Jamal Balfas and Tamsil Linrung were later released as authorities found they had not enough evidence to charge them.
A lawyer for Dwikarna pointed out alleged inconsistencies in the governments case.
Judge Henrick Gingoyon told AFP that government lawyers swiftly filed a legal comment opposing Dwikarnas motion.
Both defense and prosecution will have 10 days each to submit additional comments, Gingoyon said, expressing optimism he would be able to issue a verdict within a month.
During their brief stay in the Philippines, Dwikarna and his colleagues were alleged to have met with associates of another Indonesian, Fathur Rohman al-Ghozi, who is now serving a 12-year jail sentence here, also for illegal possession of explosives.
Al-Ghozi is an alleged explosives expert of the radical Muslim group Jemaah Islamiya, which Asian governments say has links to Osama bin Ladens al-Qaeda network. He was arrested in Manila in January.
Philippine officials allege that Dwikarna had also been implicated in bombing attacks that killed at least 22 people in Metro Manila in December 2000 and in a bomb attack on the Philippine Embassy in Indonesia in the same year in which two people were killed and Ambassador Leonides Caday was seriously wounded.
Government sources say the Philippines has been under political pressure to free Dwikarna as Islamic militants in Indonesia have voiced protests.
Foreign Affairs Secretary Blas Ople has suggested the two countries seal a prisoner-swap accord that would allow Dwikarna to serve the rest of his sentence in Indonesia.
However, Justice Secretary Hernando Perez said a swap can only take place once the court verdict becomes final.
Dwikarna admitted he was a member of the Lakas Jundullah, an Indonesian group, and was a member of a committee preparing to impose Islamic law in South Sulawesi but said this "does not mean that I am a fundamentalist or a terrorist."
He alleged there was a campaign to brand him a terrorist. AFP, Nikko Dizon