The survey, carried out by Healthcare Republic for GP newspaper, found that almost three in 10 GPs said they would not have the swine flu vaccine, with the same number, 29 per cent, unsure whether they would or not.
Out of the 216 GPs polled, more than seven in 10 said they were concerned there had not been sufficient trials.
Professor David Salisbury, the Department of Health's director of immunisation, told Healthcare Republic that front line health workers had a duty to get immunised.
"They have a duty to their patients not to infect their patients and they have a duty to their families," he said.
"I think you solve those responsibilities by being vaccinated."
A separate poll found even more GPs saying they did not want to be vaccinated, with 49 per cent saying they would reject it.
The survey for Pulse magazine, which questioned 115 doctors, said they would reject it, with almost one in 10 undecided.
More than two thirds of those who will reject it believe that the jabs have not been tested enough, while most believe swine flu has been so mild in the majority of cases that it is not needed.
Richard Hoey, editor of Pulse, said: "The medical profession has yet to be convinced by the Government's whole approach to swine flu, with most GPs now feeling that the Department of Health overreacted in its policy on blanket use of Tamiflu.
"Inevitably, that has coloured feelings about the planned immunisation campaign.
"The view among many doctors is that the Government hasn't yet made its case for why such a huge vaccination programme needs to be rushed in for what seems to be an unusually mild illness."
Another piece of research, published in the Emerging Health Threats Journal, found that parents and health workers may refuse to get immunised or vaccinate their children against swine flu.
The study conducted in Vancouver, from experts at the University of British Columbia and Simon Fraser University in Vancouver, involved 85 people before the onset of the current flu pandemic.
Parents known to favour alternative medicine were particularly opposed to vaccination, but health workers said they would be reluctant to get vaccinated if the illness was mild.
The survey results come as it was announced by the Government that 14 scientific projects into swine flu were being fast-tracked to help understand the pandemic.
The research projects, backed by £2.25 million, will launch around Britain this week, with results available by the end of the year.
The 14 projects will look at issues such as whether closing schools is effective in preventing spread of the virus and if health workers should wear face masks.
Experts will also look at managing swine flu in pregnant women to protect them and their unborn babies, and will identify priorities for looking after critical care patients.
The work will be led by research centres in Leicester, Nottingham, Newcastle, Edinburgh, Sheffield, Manchester and London.
One of the studies, led by Professor Steve Goodacre of the University of Sheffield, will look at data that can be recorded in A&E to evaluate whether somebody with swine flu needs to be admitted to hospital.
Another project will estimate how long somebody is contagious for and advise on a "safe distance" for people wishing to avoid swine flu.
Professor Jonathan Nguyen Van-Tam of the University of Nottingham and the Health Protection Agency, will lead this study.
"Very little is currently known about the H1N1 virus which makes it very hard to predict the numbers of people likely to catch it and how best to treat them," he said.
"For example, we do not know how long the virus is excreted by infected humans and how much virus is spread to surfaces and carried in the air."