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The society is urging employers to offer IT staff a choice of shorter keyboards and a range of different mice to combat the problem.
"It is not necessarily a liability issue, but it can lead to people taking time off work and that costs employers money," said Roger Haslam, chairman of the society.
Research conducted by the University of Surrey and Loughborough University, showed that the more frequently people use computers, the more likely they are to suffer aches and pains.
Computer users can develop problems such as "mouse shoulder" because they have to stretch to reach the mouse, which is usually placed at the right-hand side of a keyboard.
"The human body is not designed to adopt awkward postures for prolonged periods and work that requires this can cause aches and pains and more serious problems over a longer period," the Ergonomics Society warned.
The society recommended that IT workers take short, frequent breaks rather than longer, less frequent breaks.
Employers should also make sure equipment is properly maintained and that mice are regularly cleaned, said Haslam.