A division bench comprising Chief Justice J N Patel and Justice K S Ahluwalia passed the directive on a PIL after the state CID failed to trace the girls who went missing from the homes.
The petitioner alleged 13 minor girls went missing from a home run by an NGO near Kolkata on October 29, 2009 and 27 from a government one in West Midnapore between November 12, 2009 and March 18, 2010.
The petitioner stated there were about 108 homes in West Bengal.
The judges yesterday also directed the state Human Rights Commission to investigate the treatment of inmates at all homes run by NGOs and the government.
The WBHRC has also been directed to investigate the death of Sushila Tamang, who died at a home in Burdwan in 2011, and Guriya, who died at a home run by an NGO in Hooghly district on July 1.
The directives came on a batch of habeas corpus petitions which alleged that no step has been taken to reunite thousands of minor and adult girls, lodged in various homes run by NGOs and the state government for years, to their families.