Melaka CID Chief Senior Asst Comm Kamaluddin Kassim told The Star Online that the girl's mother, aged 30, had lodged police report on July 20.
He said police have almost completed their investigations.
The girl also claimed the boy had inserted his fingers into her vagina when the adults were away, the portal reported.
The single mother lodged a police report the next day.
The girl was later taken to Melaka Hospital on July 20 where she was warded.
Medical report revealed that there was a fresh hymen tear, the portal said.
Earlier this year, Kamaluddin said two-thirds of rape cases reported between 2012 and last year in the state involved children.
He said many of the victims consented to having sex, but the cases were deemed statutory rape due to their age.
He said lack of parental supervision was the reason for the problem.
Boy, 7, allegedly raped kindergarten girl in Melaka Astro Awani | July 27, 2017