Staff at the Telford base were told yesterday have been informed thattheir personal information was on a computer taken from a car parked at a motorway services.
One of the affected employees said staff had been informed of the theft yesterday morning.
The employee, who did not want to be named, said: "We were told that our personal details were on the stolen laptop, including our bank details.
"Given the importance of security here, you would think the company who had won this huge MoD contract would have better security procedures than this."
The laptop was taken from a car belonging to an employee of Kuehne and Nagel on Tuesday. Police said it was stolen at around 1.30pm from the boot of the car at Strensham Services on the M5 near Worcester.
The computer has been reported missing in the West Midlands area.
A spokesman for Kuehne and Nagel said: "We Kuehne and Nagel confirm that the company laptop of an employee went missing, presumed stolen, on June 2.
"The laptop was being used for preparations for the Ministry of Defence contract known as Logistics Commodities and Services (Transformation) which is due to commence on August 1 2015.
"The laptop was encrypted in line with MoD policy, but contained some personal data of civil servants currently working for the MoD, who are due to transfer to Kuehne and Nagel on service commencement.
"Kuehne and Nagel regret this potential breach of personal security which was caused by the laptop being temporarily unattended in the locked boot of an employee's car.
"The police have been informed and we are co-operating with their efforts to trace the missing laptop. The MoD has informed affected employees and advised of actions they can take to prevent their data from being misused.
"Kuehne and Nagel has also arranged a Data Breach Response Facility with Experian, which provides staff with 12 months of free credit and identity monitoring services."
Kuehne and Nagel are a Swiss-based global logistics and transportation company based in Switzerland. They have been sub-contracted to work with Leidos on supplying the Logistics Commodities and Services (Transformation) programme at MoD Donnington.
Leidos won the contract to construct a £90m defence fulfilment centre next to the logistics centre at Donnington, with another £40m to be spent on IT systems.
Hannah Carolin, a spokeswoman for the MoD, confirmed that a laptop belonging to a commercial company that contained encrypted HR information about MoD personnel has been reported missing in the West Midlands.
She said: "We take the protection of our people, including their personal data, extremely seriously and although the data will be difficult to access given the encryption protection, we have informed our employees and are working to support them."
"There is an ongoing civilian police investigation into this matter, so it would be inappropriate for us to comment further at this time."