Indonesia has condemned a small protest "in the strongest terms" after an activist broke into its consulate in Melbourne on Friday and held up the West Papuan flag.

Indonesia's Foreign Ministry has requested Australia take action to prevent a similar incident happening, highlighting the sometimes delicate relationship between the two countries.

The West Papuan flag Credit:Reuters

Earlier this week, Indonesia temporarily suspended military ties with Australia over material taught at an army base in Perth. The teaching material related to sensitive issues for Indonesia, including West Papua's bid for independence.

Indonesia has since backed down on the suspension. However, its military chief Gatot Nurmantyo maintains the curriculum taught at the Perth army barracks is "too painful to explain" because it allegedly discredited Indonesia's military.