The Defence Ministry on Saturday denied media reports of theft of three computer hard disks from the tri-service Integrated Defence Staff (IDS) headquarters at the Kashmir House.
A release said there had been no data theft as alleged in a newspaper report.
It, however, said that 13 printer ink cartridges worth Rs 17,000 were missing from the storekeeper's table drawer.
"The police station in Chanakyapuri had been informed about the incident and a First Information Report (FIR) was lodged on July 25," it said.
The ministry also said that the incident was being viewed seriously and a Court of Inquiry had been ordered. Action would be initiated after the inquiry report.
The IDS, which is the strategic think tank of the three armed forces, had filed the complaint.
The theft of printer cartridges comes barely a month after the unprecedented security breach at the National Security Council Secretariat involving suspected cyber-espionage.
Leakage of classified documents from the war room of the Naval Directorate in 2005 had led to the arrest of several Naval officers and businessmen.
Investigations by the Central Bureau of Investigation (CBI) have indicated the presence of a ring of officials in the armed forces and the ministry of defence who may be supplying sensitive information to businessmen and former Naval officers.