Following the Moro conflict and subsequent major military operation in the islands of Mindanao during the administration of President Ferdinand Marcos in 1970s,[8] thousands of Filipinos mainly from the Moro ancestry have sought refuge in neighbouring countries of Malaysia, Indonesia and Brunei, with majority of them mostly heading to the state of Sabah in Malaysia.

[9][10] In addition to armed conflict in the southern Philippines, many Filipinos flee due to economic factors and hope for a better lives.

[2][11] Although unlike the economically motivated illegal immigrants, the Filipino refugees have long been granted special permission to stay despite limited access to the state employment, social services and public amenities.

As there is still no definite sign the conflict will permanently stopped, the influx of Filipino refugees continued even after the peace agreement with the Moro National Liberation Front (MNLF) in 1976.

[6] Following the government decision to issue residency visas and a special card known as the IMM13 to the refugees, the UNHCR closed its office in 1987 after operating for 10 years.

Recent findings in 2014 found there are at least 544 Filipino refugees (mostly from the Bajau community) taking shelter in Derawan Island, Berau Regency, East Kalimantan.

[16] Responding to the report, Indonesian President Joko Widodo ordering them to be sent back to their country in the Philippines immediately,[17] although it is still unknown whether the process of deportation has begun.

[38] The huge Filipino refugee settlements in Sabah have mainly criticised by the locals there for contributing to the significant rise of rampant crimes,[39] with the refugees loyalty towards the country they seeking for refuge are also been questioned for the unstoppable crimes perpetrated from their own community[40] as a Filipino man was recently charged in court as recently in 2017 for supporting the ideology of Abu Sayyaf terrorist group.

[42] This was done to counter-act reconquest attempts by the Philippine centered Sultanate of Sulu, which used to rule Sabah, before sovereignty was transferred to Malaysia.