If approved, the plan would include Indonesian Agus Dwikarna, who last month was jailed for at least 17 years in the Philippines for possessing explosives.
Ople said he explained the proposal during a meeting with Megawati.
"I explained a bit the Philippine proposal and said it has been officially submitted to the ministry of foreign affairs. She said it looked like a good idea," he told reporters.
Dwikarna was arrested at the Ninoy Aquino International Airport in March. Two other Indonesians arrested with him have since been freed without charge and sent home.
"I told (President Megawati) that Dwikarna is enjoying all his rights and is being treated humanely in the Philippines," Ople said.
Ople said Indonesian officials still needed time to study the proposal to exchange convicted prisoners before it could become an official agreement.
Justice Secretary Hernando Perez, however, said Dwikarna cannot be turned over to Indonesia while his conviction is not yet upheld by the Supreme Court.
Under criminal procedures, presidential prerogative or executive clemency like pardon, parole or commutation of sentence can only be exercised once the conviction becomes final or has been affirmed by the High Court.
Pasay City Judge Henrick Gingoyon sentenced Dwikarna, a suspected member of Jama’ah Islamiyah believed to have ties with Osama bin Laden’s al-Qaeda terrorist network, to 17 years in jail last July.
In Manila, a senior foreign department source said sending Dwikarna home was intended to placate his allies and discourage them from harming Filipinos living and working in Indonesia. — AFP, Delon Porcalla