Hackers are thought to have planted a Trojan in the computer systems at Houston and used the infection to ride the satellite uplink to the Space Station.
The problem has been complicated by the onboard computer systems, which are running older software, including legacy code such as Windows 3.1.
Microsoft has said that there is nothing it can do since the operating system is no longer supported with security fixes.
"I am sorry but there is nothing we can do. It is past its deadline," said Professor Brian Offin, Microsoft's head of obsolete operating systems.
"Windows 3.1 is a very old operating system and the technical support team has been entirely subsumed into the Vista troubleshooting team and trust me, they are needed there."
Professor Offin added that Microsoft is not blind to the plight of the astronauts and is searching personnel files for staff who worked on the code, but have since retired and may have time to deal with the problem.
There is no life threatening danger to the astronauts as yet, but the escape capsule that can carry them home has been warmed up and is ready to go, despite concerns that hackers might have reprogrammed that too.
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