Contrast between background and text, site navigation and use of colours all have an effect on how effectively disabled people can use particular websites.
Adam Field, from the university's School of Electronics and Computer Science, conducted the survey.
He explained that even if a website looked fine and was error-free, it did not mean that it would work with all browsers and for all users and may not always be accessible for visually impaired people.
The aim is for websites to function with any browser and any size screen, which can happen if site developers follow the proper guidelines.
Mr Field said: "There is a big push within government to improve web accessibility. Although 61% of sites do not comply with the Web Content Accessibility Guide, the 39% which do is encouraging."
However, he expressed surprise at the number of websites found with HTML errors.
Flagship website
Mr Field said: "It is a very unfortunate statistic. It should be better. It is not something that is difficult to improve upon.
"The accessibility issues are a lot more difficult to sort out."
Mr Field also pointed out disabled people were likely to require government services and, therefore, had even more reason to want to use government websites.
Organisers of a leading conference, WWW2006, have called on webmasters from UK local authority and central government to increase their understanding of the latest web standards.
A spokesman for the Cabinet Office said there were excellent examples of eAccessibility in the public sector. He drew attention to the flagship Directgov website, which lists all public services in one place, and which meets the high demands of the AA standard.
He told the BBC News website: "The Cabinet Office has been active in promoting better accessibility of government websites.
"It has published detailed guidelines for UK government departments and it has raised the visibility of the issue across the EU by sponsoring a detailed study on eAccessibility of EU government websites carried out by RNIB and others.
"One difficulty is that many authoring tools do not generate compliant HTML and make it difficult to edit the coding.
"This is an issue that the IT industry must address and we are working with them on that," said the spokesman.
