The decision to patrol the Sulu and Celebes seas, which together form a key waterway between the three countries, comes just over a week after the southern Philippines-based Abu Sayyaf beheaded a Canadian captive.
Abu Sayyaf gangs have earned many millions of dollars from kidnapping foreigners and locals in the region since the early 1990s.
Ten Indonesian sailors were abducted off the southern Philippines by Abu Sayyaf in March, but returned home last week after being freed.
The Sulu and Celebes seas are used for the passage of 55 million metric tonnes of goods and over 18 million people per year.
The three countries also agreed to set up a hotline to communicate faster during emergency situations, improve coordination when giving assistance to people and ships in distress as well as intensifying information and intelligence sharing.
"We recognised that threats from armed robberies against ships, kidnapping and other trans-national crimes if not addressed appropriately can undermine the confidence in trade and commerce in our region," Marsudi added.
Abu Sayyaf is believed to have just a few hundred militants but has withstood repeated US-backed military offensives against it, using the mountainous jungle terrain of Jolo and nearby islands to its advantage.
Although its leaders have pledged allegiance to the Islamic State (IS) group, analysts say they are more focused on lucrative kidnappings-for-ransom than on setting up a caliphate.