Human resources managers are becoming increasingly worried about the number of junior doctors still working without contracts.
They say the situation breaches employment law and could leave trusts vulnerable to tribunals.
The British Medical Association has expressed concerns about the problem, which could be affecting thousands of junior doctors who took up posts in August but have yet to receive employment contracts.
One HR manager, who asked not to be named, said her trust had at least 15 doctors appointed through the Mersey Deanery without a contract.
One had been employed twice without his knowledge, once on a so-called Hewitt contract, where doctors in post are given a temporary contract, and then again on a permanent contract. He had been paid twice as a result.
The manager said: 'Employment law says contracts have to be issued within four weeks. If you are working without a contract you are in theory working illegally and do not have employee rights.
'If you are an employer you have no right to receive notice from employees and you could be taken to industrial tribunal.'
No other group of staff would be treated in this way, she added.
An NHS Employers spokesperson said: 'The BMA has expressed concern to us about delays in some trusts issuing written employment contracts to their junior doctors.'
She said some contracts had been delayed as a result of the workload caused by the increased number of junior doctor appointments this year.
The Mersey Deanery declined to comment.
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