The documents, containing CAG's remarks, have been filed before a bench headed by Chief Justice R M Lodha in connection with a case relating to missing of an official of the museum who has also highlighted the financial irregularities before he went missing.
"The CAG report raises questions as to how antiquities of national importance reach viz. auction houses viz. Sotheby's, Christie's, etc," the documents said.
These documents were filed in a pending habeas corpus petition (a plea filed to secure presence of missing persons) in which the apex court has already sought West Bengal government's response on the whereabouts of whistleblower Sunil Kumar Upadhaya.
It said the CAG report is a part of Performance Audit of Preservation and Conservation of Monuments and Antiquities the Ministry of Culture conducted in 2013.
The petition, filed by a relative of Upadhaya, said that several RTI applications regarding the investigation in the missing of Kolkata museum's preservation officer were filed with West Bengal Police but no satisfactory reply has been received.
The documents, filed through advocate Anirudh Sharma, said the observations in the CAG report have "unequivocally" observed significant discrepancies in the number of antiquities reportedly available in the Indian Museum.
The lawyer said that in respect to Indian Museum, Kolkata, the CAG report has stated that no standard system for purchases and acquisition of antiquities by way of gifts was there.
Krishan Mohan Upadhaya, a Ghaziabad resident who had moved the court in the case, also said that the CAG report has also raised questions on authenticity of the artefacts.
"No assurances of authenticity of artefacts as there exists no system for evaluation of acquired objects," the document said.
"The CAG has observed significant discrepancies in the number of antiquities possessed by the Indian Museum and National Museum, for Indian Museums and had said that fake coins were being displayed officially," it said.
The petitioner also highlighted the exceptions taken in the CAG report over diversion of funds from plan head to non-plan head and irregularities in expenditure. "In Indian Museum, out of 29 galleries, 14 were not covered under CCTV surveillance.
Even the installed cameras were operational only during working hours. Thus there was no surveillance during night," the petitioner, referring the CAG report, said.
It has been alleged that the officer has been missing since July 3 after he mentioned the alleged irregularities in the management of the museum.
"It was an open secret now in public discourse that he had raised his voice against corruption and irregularities prevailing in Indian Museum for which he has paid a price," the plea had said.
"Dr Sunil Kumar Upadhyay working as a preservation officer in Indian Museum, since July 3, 2014, and missing report was lodged on July 4, 2014 which was converted into FIR only on July 19, 2014 not by Kolkata Police itself but on a written request by his brother.
"It now transpires that a complex investigation by an expert investigating agency would be required, having seamless jurisdiction and will to take on the local mafia dealing in artifacts," it had said.