The two countries first inked the defence cooperation deal in 2010, agreeing to share military intelligence, give logistical support and coordinate security operations.
But while Indonesia ratified the document years ago, Papua New Guinea's parliament only did so on February 14, with the government formally bringing it into force a week later.
Papua New Guinea has had difficult relations with Indonesia since Jakarta annexed West Papua following a contested vote of tribal representatives in 1969.
The pro-independence Free Papua Movement has waged a low-level insurgency with Indonesian military for decades, leading to refugees, Indonesian forces and rebels crossing West Papua's long border with Papua New Guinea.
"Security is a cornerstone of trade, investment and business," Papua New Guinea Foreign Minister Justin Tkatchenko said in this week's statement.
"In PNG we hope to speak to our security challenges... along our 800-kilometre (500-mile) border corridor," he said.
This would help build "some of our security capabilities and capacities", he added.
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