The girls, both stated to be around 17 years of age, were found hanging with a cloth from a water supply pipe inside the high-security shelter home, managed by the Department of Women and Child Welfare, yesterday.
The duo had allegedly escaped from the Nari Niketan on June 23 by scaling the wall, but were brought back the next day after being spotted at Kaithal district.
However, they were found missing again yesterday during the evening roll call.
They were later spotted hanging inside the bathroom after a search was launched by the staff to trace them out.
The district administration had ordered a probe to be conducted by a Sub Divisional Magistrate to ascertain the cause behind the deaths.