GP leaders said the profession was still adapting to the forms, but warned that employers should consult occupational health advisers on support for patients to get back to work.
A report by Crohn's and Colitis UK said better use should be made of the 'may be fit for work' section of fit notes to tell employers about changes they can make to help people work.
The charity interviewed 1,906 people with inflammatory bowel disease (IBD).
More than 80 per cent said they worried about managing their symptoms when thinking about future employment.
Half had already ruled out career options because of their IBD and 69 per cent said the condition had preventing them from reaching their full educational potential.
Crohn's and Colitis UK is calling for a programme of information for employers to help them understand the needs of people with IBD and other long-term conditions.
It has called for GPs to make full use of fit notes to indicate the fluctuating nature of symptoms and include recommendations for reasonable adjustments to help people work.
The charity is calling for GP commissioners to understand how important work can be to people with IBD, and the impact the condition can have on their working lives.
Sections five and six of the fit note allow GPs to describe changes to hours, duties and workplace to help people return to work.
Derbyshire LMC secretary Dr John Grenville said he would have 'no problem' putting details on fit notes about what the patients may need to help them back to work.
But he pointed out that fit notes were 'short certificates' and that employers should treat a note from a GP as a signal that they should consult an occupational health provider to assess how to help employees.
He added: 'I think some GPs may not think of this at the moment, and patients also may want a sick note, not a fit note. I think it is something we are learning.'