The incident came to notice this morning when volunteers of Sewadal found the two inmates -- Munni, 18, and Pooja, 20 -- missing from their room.
The facility, run by NGO 'Hari Om Sewadal', houses some of the inmates of the infamous Apna Ghar shelter house.
These inmates were brought here following a surprise raid that was carried out at the Apna Ghar by a team of National Commission for Protection of Child Rights (NCPCR) after cases of abuse and maltreatment of inmates came to light.
Meanwhile, Rohtak DSP (Headquarter) Sumit Kumar along with police officials rushed to the shelter house at Gandhi Nagar locality here and recorded statements of office bearers of the Sewadal.
"We have formed 10 teams which are simultaneously carrying out raids to find the girl inmates," the DSP said, adding that no case has been registered so far in this regard.
Police said Munni hails from Guwahati and had given vital information about functioning of the Apna Ghar caretakers to CBI officials during the central agency's investigation.
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CBI is currently probing the Apna Ghar shelter home case.
The Apna Ghar shelter house, run by NGO 'Bharat Vikas Sangh', had landed in controversy when a team of NCPCR had rescued over 100 inmates, including children, girls and women, after carrying out a surprise raid there. The inmates had levelled serious allegations against caretakers of the facility.
The Haryana government had sealed the Apna Ghar shelter home in June after the sexual and physical assault of over 100 women and children was exposed.