Indonesia and the Philippines have signed an agreement to share intelligence resources to more effectively combat drug trafficking along the two nations' porous borders.

The agreement came amid Manila's efforts to prevent the execution of a Filipina convicted of drug smuggling in Indonesia.

In a memorandum of understanding signed during Indonesian President Joko Widodo's first state visit to the Philippines, the anti-narcotics agencies of the two countries agreed to exchange information on new drug trafficking methods, and the latest and emerging forms of illegal drugs, as well as the new routes that smugglers use.

"The Philippines and Indonesia have pledged to work together to liberate their territories from the clutches of the drug menace," director-general Arturo Cacdac of the Philippine Drug Enforcement Agency said after signing the memorandum.

Joko was in the Philippines yesterday to wrap up a three-nation trip across Southeast Asia. He had been to Malaysia and Brunei.

Despite the focus on drug trafficking, Joko and his host Benigno Aquino did not discuss the fate of the woman, who has not been publicly named, facing death by firing squad in Indonesia for allegedly trafficking 2.6kg of heroin. Manila is seeking a review of her case.

In a statement issued before the talks, Philippine Vice-President Jejomar Binay said the Philippines "has taken the proper legal steps in accordance with Indonesian laws".

"We assure everyone that your government will extend all needed assistance to our kababayan (countryman)," said Binay, whose office oversees Filipinos abroad.

Joko's government recently executed six convicted drug smugglers and is preparing to execute 11 more - among them foreigners.

Joko and Aquino also sidestepped the issue of China.

Indonesia and Singapore have played pivotal roles in pushing forward a "code of conduct" meant to ease tensions between China and other states, including the Philippines - all with varying territorial claims over the South China Sea.

China has been building island fortresses across a wide swathe of the sea where it has control, sparking protests from the Philippines, which has sued Beijing at an international court to assert its claims.

Indonesia and the Philippines instead focused on resolving their own border issues.

They agreed to resume negotiations started in October last year on overlapping portions of the continental shelf in the Mindanao Sea and Celebes Sea.

Discussions on the continental shelf began five months after Manila and Jakarta agreed to draw a boundary between their overlapping exclusive economic zones.

That maritime agreement was hailed as historic and a model for resolving border issues among neighbours in East Asia.

Joko's state visit came while he is in the dilemma of whether to cancel the nomination of a police chief whose reputation is in doubt following accusations by Indonesia's corruption watchdog.

Aquino, meanwhile, is also parrying plots to oust him over the death of 44 police commandos during a disastrous police raid to capture Malaysian terrorist Zulkifli Hir, better known as Marwan. (***)