A team of police officials are investigating the incident to find out if the children were victims of child trafficking.
The brother of the two girls was working in Bangalore. He received an SMS from his 16-year-old sister that the family had been kept in confinement at a house in Singanallur police limits by R Lalngaikung, 47, from NC Hills in Assam.
Singanallur police inspector P Maheswaran and his team rescued the girls and their mother on Monday night.
Police said, Lalngaikung, who runs an NGO, tried to have the children admitted at Michael Job Orphanage at Sulur on June 1. However, they were unable to gain admission.
A frustrated Lalngaikung allegedly treated the children badly which prompted the elder of the girls to message her brother for help.
The two girls and their mother were sheltered at a home in the city. "We inquired with the children who had given statements that they were not harassed by the man who brought them here. Thus, we sent them back to Singanallur police for further investigation," said P Samson, Chariman of CWC.
Meanwhile, the police took Lalngaikung to the police station for inquiry. However, the girls and their mother were not ready to file a complaint against him and he was let off. Members of the CWC have now decided to send the trio back to Meghalaya.
Two years ago, 42 girls including 23 from Nepal, were rescued from Michael Job Orphanage by district child welfare committee volunteers.
The raid took place after the Nepal embassy sought help from the Indian government to trace and rescue 50 Nepali girls who had gone missing from the country. Twenty-three of the missing girls were being kept at an orphanage.