Many of the thousands of undocumented workers had left Mindanao, hoping to escape a life of poverty and war.
Thousands of Filipinos have been deported from Malaysia in the past few weeks as part of the Philippine government's "gradual repatriation" programme.
For decades, Filipinos have been illegally crossing into Sabah, eastern Malaysia, in search of a better life.
In November 2016, President Rodrigo Duterte signed a deal with Najib Razak, Malaysia's prime minister, that allowed mass deportation of undocumented Filipinos in Sabah.
Most of those deported in the past few weeks are from Mindanao, from where they had to move to Malaysia hoping to escape a life of poverty and war.
"Money is good in Sabah. Even with menial jobs, I earn. Not like in Sulu where I am from," Jessica Ali, who has been travelling to Sabah illegally since she was four, said.
Ali has been deported several times. Last year, she was arrested while pregnant and gave birth in detention.
Malaysia has been arresting and deporting undocumented Filipinos for decades. There have also been reports of abuses suffered by Filipinos while in detention.
Duterte had promised to revive the Philippines' dormant claim to Sabah during his campaign last year.
However, that issue was not part of the agenda during his first state visit to Kuala Lumpur last year.
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