The computer contains the names, addresses, bank details, National Insurance numbers and pay rates of 500 employees at the attraction.
It was stolen from a car of an employee who works for Moorepay Ltd, who handle the attraction's payroll.
The company, which is based in Hampshire, was unavailable for comment.
Tim Smit, Eden's creator, said: ''A computer containing the personal details of employees of a number of companies, including the Eden Project Ltd, has been stolen from the car of an employee working for a contracted payroll company.
''Suffice to say we are appalled at the lapse of security and are making sure that our personal data is never put in such a vulnerable position again.''
Police investigating the 1 June theft are monitoring bank accounts of employees.
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