Superintendent of Police (North) Vijay Singh told PTI that the enquiry would be conducted against Stop Child Abuse Now (SCAN) NGO, which receives funding specially from the UK, with the caretakers alleging that some of the children were pushed into crime when they were in the custody of the NGO.
SCAN, is a project of El-Shadaai, an organisation which receives fundings from outside the country.
The caretakers attached to 'Apna Ghar', a government-run shelter home for children managed by the Directorate of Women and Child Welfare, had alleged that two of the four children arrested by police recently for robberies were in custody of SCAN which had taken them from the protective home for rehabilitation.
They had demanded a police enquiry into the matter.
Porvorim police had arrested four children, an alleged gangster and a caretaker in connection with the nexus involving the staffers and gangsters.
According to police, the juveniles were used in crimes like robbing vehicles and their involvement was even found in a murder case.
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Meanwhile, the Directorate of Women and Child Welfare supported the NGO saying there was nothing to be probed into the matter.
"The children were in the NGO custody when they were arrested and not when they were involved in robbery", Sanjiv Gadkar, Director of Women and Child Welfare said.
Earlier, Chief Minister Manohar Parrikar had asked the police to file an FIR against six caretakers, who were allegedly involved in letting the children escape from the remand home.