President Duterte's administration has ordered a ban on the deployment of overseas foreign workers to Kuwait after the deaths of several women, including 29-year-old Joanna Demafelis.
Demafelis' body was found in the freezer of her employers' home on Wednesday where authorities believe it could have been stored for up to one year.
The offer of a free flight home was extended to the 10,000 Filipinos who had overstayed their visa in the Gulf state.
"I will sell my soul to the devil to look for money so that you can come home and live comfortably here," Duterte said Tuesday. The Philippines President said last week he was ready to take "drastic steps" to protect Filipinos working abroad.
As of Wednesday, more than 900 Philippines workers had returned on chartered flights, the country's Overseas Workers Welfare Administration told CNN.
"They will return bringing with them virtually nothing but sad stories of how their dreams for a better life for their loved ones got shattered by exploitation and abuse. They are the first of hundreds who have heeded the President's call for them to go home so they could escape further maltreatment abroad," Philippines Foreign Secretary Alan Peter Cayetano said on Facebook.
Kuwait has become a popular destination for Philippines overseas foreign workers in recent years.
Duterte previously said he plans to visit Kuwait and take up the issue.
"To the Kuwaiti government and all others where our OFWs work, we seek and expect your assistance in this regard."
When asked for comment, Kuwaiti Deputy Secretary of State for Consular Affairs Sami Abdul Azizi told CNN he has met with Philippine Ambassador Renato Pedro Villa to discuss issues pertaining to the Philippine community living in Kuwait, but declined to give further details.
They said she never said anything bad about her employers, but had suspicions she was being watched. Demafelis was only able to speak to them three times a year.
During that last phone call, Demafelis said she planned to come home in 2018. But after not hearing from her for a nearly year, Demafelis' family reported her missing, her sister told CNN Philippines.
Investigators tried to find her through the Kuwaiti agency that recruited her, but discovered it had closed down.
CNN's Mohammed Tawfeeq and Sandi Sidhu contributed to this report