Just two per cent of respondents told Hospital Doctor magazine that their morale was 'excellent', with 54 per cent describing their morale as 'poor' or 'terrible'.
Almost three quarters of the 1,400 doctors quizzed by the magazine added that their spirits had worsened during the last year.
In response the Department of Health said that the survey results were not consistent with the more detailed research undertaken by the Healthcare Commission, which claimed that 73.3 per cent of staff were satisfied with their work.
But Stephen Campion, chief executive of the Hospital Consultants and Specialist Association, said he was "saddened" by the results.
"Traditionally, many doctors have followed in their parents' footsteps and increasingly we are hearing doctors saying they wished they hadn't recommended a career in medicine to their children," he continued.
"This is indicative of the extreme frustration and low morale hospital doctors are feeling."
The British Medical Association's Dr Jonathan Fielden, chairman of the association's consultants' committee, commented: "The results of this survey show how demoralised so many doctors are feeling and how they believe constant government reforms and targets are taking them further away from their initial vocation to treat patients."
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