Malaysia is a magnet for migrant workers but salaries are low and employees are not protected by labour laws.
In recent years the country has seen a series of cases involving mistreatment of domestic workers including deaths.
Police identified the victim as a 21-year-old called Adelina who had been working in Malaysia for two years.
Her head and face were swollen and she had wounds to her hand and legs, a police document said.
A woman and her brother, both in their 30s, are under investigation following the deatht in northern Penang state, local police chief Nik Ros Azhan Nik Abdul Hamid told AFP.
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Malaysia relies on an estimated two million Indonesians who toil in plantations, in construction, in factories and in homes -- both legally and illegally.
In 2014 a Malaysian couple were sentenced to hang for starving their Indonesian maid to death.
Two years earlier a Cambodian maid was starved to death by her employers, who received a 24-year jail sentence.
Malaysia has taken some steps to improve the welfare of domestic workers, including requiring them to have at least one day off a week and increasing minimum monthly salaries to 700 ringgit ($176). But activists say enforcement is difficult.