The BMA said it was 'concerned' by the findings and that more must be done to combat the problem.
The GMC’s National Training Survey 2013, published on 5 December, surveyed 54,000 doctors in training in the UK.
It found that one in five trainee doctors have witnessed someone being bullied in their current training post.
A total of 6,620 trainee doctors in 2013 – 13.2% of 49,990 who answered the question - had been a victim of bullying while in their training post. Of these, 44.3% described the source of the bullying or undermining behaviour as their consultant or GP trainer.
The most common bullying or undermining behaviours reported were ‘persistent and deliberate belittling or humiliation’ and ‘shouting, threatening or insulting behaviour’.
The BMA’s junior doctors’ committee co-chairwoman, Dr Kitty Mohan, said: ‘It is concerning that one in ten junior doctors reported that they had suffered from bullying or harassment and that two in ten had witnessed a colleague suffering the same treatment.
‘We must do more to combat any environment that allows bullying or harassment by encouraging NHS staff to share their concerns immediately. Junior doctors have a right to carry out their job in a workplace that is free from any form of intimidation.
‘To guarantee patient safety, we must establish a culture where the NHS actively listens to its workforce and acts upon any concerns raised.'
GMC chief executive Niall Dickson said more needs to be done to support trainees. ‘The best care is always given by professionals who are supported and encouraged,’ he said.
‘The survey provides us and employers with crucial information about the quality of the training environment, which is also where patients receive care and treatment. These doctors are in an ideal position to alert us to potential problems and employers will also want to reflect on these results.
‘Patient safety remains our top priority and all doctors irrespective of their seniority should feel supported in improving the standards of care for their patients.’