The matter relates to the issue of children being trafficked from an orphanage in West Bengal.
The top court said it is not bothered about the Centre or state commissions but about the girl victims.
Coming down heavily on the two commissions, a bench of Justices Deepak Gupta and Aniruddha Bose said it is very unfortunate that two statutory bodies are fighting like this in a trafficking case.
The bench also said that it is very sad that the two commissions can not find conclusion for the welfare of the children.
The court listed the case for further hearing on Wednesday.
The apex court was hearing a petition filed by the NCPCR against an earlier Calcutta High Court ruling in which the court restrained the national child rights body from getting involved in the issue of child trafficking in West Bengal since the state commission had already been apprised of the situation.
The National Commission had asked Additional Director General of Police (ADGP), CID, West Bengal Police Rajesh Kumar to ascertain the facts related to trafficking in an orphanage in Jalpaiguri.
The officer had moved the Calcutta High Court and sought to restrain the NCPCR from further proceeding in the matter, saying that it was already being monitored by the state commission.
The High Court on August 29, 2017 restrained the NCPCR from proceeding further in the matter. Thereafter, the NCPCR moved the top court against the order.
( With inputs from IANS )