Apparently in view of the development, an advisory has been issued to the Services that computers having internet facility should be kept at a distance from those on which classified work is conducted.
The security breach took place in December and was detected by the intelligence agencies after which a high-level probe was ordered, government sources said here.
The computers that were hacked are located in the South Block and belong mainly to the Army along with the other two forces, they said.
The security establishment fears that up to 30 files marked as classified could have been compromised in the process, the sources said.
National Security Advisor Shivshankar Menon sought to downplay the hacking incident saying there are "various forms of compromise" and "not every leaked password is a big threat to security.
"A mere fact that some computer is open in North Block and South Block and is accessible, does not mean that therefore there is big gap in security."
Insisting that "things are not in bad shape", he said, "We will deal with those computers which we feel are compromised."
An advisory issued to the Services said that it was found that a spyware was detected which could read the files of computers, which were not even connected to internet, the sources said.
Armed forces have suffered a lot due to the attempts of hacking by Chinese and Pakistani hackers as one Major posted in Andaman and Nicobar Islands was found to have leaked critical information from his computer.