They face up to 35 years in jail and whipping if convicted for both offenses.
Chuah said Marsini, who started working for the couple in January, managed to escape from her employers and lodged a police report. He said she is currently in a shelter home to nurse her injuries.
The couple has been freed on bail, with a court date set for Oct. 16.
Indonesian Embassy officials could not be reached immediately for comment.
More than 200,000 Indonesian maids work in Malaysia. Indonesian officials say hundreds complain every year of mistreatment, overwork and unpaid salaries.