The accused, Poonamchand Malviya, has been arrested and sent to judicial custody by a court in Khandwa based on the complaint lodged by the girls, City Superintendent of Police (CSP) S N Tiwari said.
While one sister is 13 years old, another one is 15 years old. Both of them were staying in the shelter home for the differently-abled, where Malviya is the director, police said.
"According to the younger of the two sisters, on Sunday night Malviya called her to his room on the pretext of giving her food and sexually assaulted her when she went there," Mr Tiwari said.
"Both the girls escaped from the shelter home late on Sunday night after crossing over the boundary wall and reached Kotwali police station," he added.
"Based on their complaint, a case was registered against the accused under IPC section 376 (rape) and the relevant sections of Protection of Children from Sexual Offences (POCSO) Act," Sonu Sitole said.
The medical examination of both the sisters confirmed that they were raped, she said.