We utilise an external ergonomic specialist company to come in and do DSE Assessments for employees and they arrange special chairs or equipment for them as required. We have seen a recent influx in employees wanting specialist chairs due to medical issues and the specialist firm have recommended that we obtain a Doctors certificate from the employee prior to purchasing the equipment. They had advised it is so we can be sure the employee does have a medical issue and that the Doctor is aware in case the issue is part of a wider medical problem. 

Is this normal practice and is it something we have to do as some employees aren’t particularly happy about going to their doctor for a certificate?

Yes - it is standard practice, partly so that you can put on record why they have the special equipment and partly to be sure that if you buy special equipment it is actually addressing their problem appropriately.  For some issues it is obvious, eg exceptionally tall or small, very petite or overweight but some issues like back or joint problems are hidden and not so obvious so you need at least a doctor's certificate or better still a specialist assessment from an occupational physician to be sure that any specialist equipment you obtain will be correct.