A poll commissioned by Sparks, a children's medical research charity, found eight out of 10 professionals believe the government is not funding its fair share of paediatric medical research.
A similar proportion suggested the pharmaceutical industry pays less attention to funding medical research for babies and children because it is less profitable than investing in drug research into conditions that affect adults.
Dr Simon Newell, consultant and senior clinical lecturer in paediatrics at Leeds St James's University Hospital, said: "This is an important survey of paediatric medical professionals.
"It gives a clear message that children's medical research is badly under-funded, although that research is vitally important to provide the basis for clinical care.
"This is a challenge that can only grow in the face of the current economic conditions.
"The key issue is that children's medical research, done well, is costly. Further money is urgently needed for research and the findings demonstrate that problems with funding is the commonest reason cited in the survey for inhibiting progress."