The two are missing since last night, they said.
The staff of the shelter home near Jhandewalan Metro station reported the matter to the Mandir Marg police station this morning.
A few days ago, the girls were found wandering at the New Delhi railway station and brought to the shelter home by members of the child welfare committee.
The girls' families were traced to Sahasrsa in Bihar and Rewa in Madhya Pradesh and were informed.
The girl from Sahrsa was brought to the shelter home on May 2 while the other two days later, police said.
A case of kidnapping has been registered as the girls are likely to be influenced by someone to disappear, a senior police officer said.
