The mother's attorney says the charges result from a difference in cultures TheLocal.se reported.
The indictment charges Azizul Raheem Awalludin and his wife, Shalwati Nurshal, with gross violation of their children's integrity.
The couple has been jailed since their arrests in December, and Nurshal attorney Kristofer Stahre said his client welcomed the charges because she would finally have a chance to defend herself.
"She hasn't done any of the things of which she's been accused," Stahre said.
Trial is set for Feb. 18.
The attorney claimed the charges were caused by a "clash of cultures." Sweden abolished corporal punishment in 1979. In Malaysia, a Muslim-majority country, the hitting of children is allowed in schools.
The children were taken by Swedish social services. They returned to Malaysia in early February.
Awalludin works for Tourism Malaysia and Nurshal is a secondary school teacher on unpaid leave. The Swedish foreign ministry says the couple, who have lived in Sweden for three years, are not diplomats.