The thieves took dozens of "hard disks" - the computer's databank - in the raid on the central London offices. They also smashed computers on four different floors.
The serious breach of security, which was discovered in the early hours of yesterday morning, may have resulted in the destruction of thousands of important and confidential files. There is concern that the move may mark a new phase in the tactics of environmental activists.
Among the computers that were ransacked were those of Brian Mawhinney, the Secretary of State for Transport, and transport ministers, Steven Norris, John Watts and Viscount Goschen.
Ministry of Defence police yesterday launched an investigation. Both the transport department and the MoD were unwilling to release details of the incident.
The transport department yesterday played down the break-in at its Marsham Street offices and insisted it was a professional burglary to steal computer parts. It also insisted that no "sensitive" documents were stolen.
It is extremely unlikely, however, that the burglars would have risked breaking into a government building to steal equipment worth a few hundred pounds. Although computer theft is a booming industry, the hard disks are awkward to remove, difficult to resell, and have a very low second- hand value. The disks costs as little as £120 to buy new.
The department uses an IBM computer system in which all material written is automatically saved on the "hard disk". It would therefore be possible to retrieve all the information kept in the machines. Material that is deleted can also be retrieved from the hard disk for several weeks before it is completely erased.
Further evidence that suggests the department was deliberately targeted is that Department of Environment offices, which are also based in the building, were left untouched. The vandals attacked floors containing the ministers' offices, the press offices, as well as finance and administration. These are based on the 12th, 13th and 16th floors - not the easiest and most obvious choice for a casual thief.
A transport departmentsource said: "It's a real mess they have ripped the innards out of all these computers. They have gone for the hard disks."
The building is protected by security guards from a government agency, the Security Facilities Executive, and closed circuit television. Film from the cameras is being examined by the police along with forensic material.
The break-in was discovered by a security patrol in the south tower of the building. The intruders did not break into the Secretary of State's personal office, where there are no computers, but did vandalise his machines in the outer office.
A transport department spokesman said it had a policy that all sensitive work should be locked in security cabinets before staff left at the end of each day.
He said the cabinets did not appear to have been touched by the thieves. He could not give details about which computer files had been lost.
A transport department spokesman said: "A number of computers were vandalised and parts taken. Some machines had been thrown on to the floor."
He added: "We will be looking to see exactly what went wrong and each department is holding its own investigation."Reuse content