The girls belong to Nari Niketan shelter home.
While one went missing on Sunday, the other two where found missing last night, police said.
Karnal Deputy Commissioner Renu Phulia and SP Shashank Anand today visited Nari Niketan at Karnal, about 130 km from here.
Though none of the three girls have been rescued as yet, Anand claimed the whereabouts of one have been traced.
A special team had been constituted to rescue the three girls, he said.
A probe had also been ordered by the Karnal district administration to check out the circumstances under which the inmates had gone missing from the complex, which remains under security.
The girls who have gone missing hail from Allahbad, Charki Dadri in Sirsa and Jhajjar.
The Nari Niketan, where some inmates of Rohtak's Apna Ghar shelter home have also been kept, houses girls including those rescued from flesh trade rackets.
Meanwhile, police have registered a case in the Nari Niketan incident.
Chandigarh: Close on the heels of Rohtak's Apna Ghar shelter home controversy, three girl inmates of a shelter home in Haryana's Karnal town have gone missing under mysterious circumstances, police said here on Tuesday.
First Published: Wednesday, July 25, 2012, 00:14