Doctors are being asked to think about the long term effect of writing a sick note for patients with potentially chronic illnesses.
Departmental guidelines on how best to certify patients are being issued this week after six months of research.
Under the guidelines, GPs are given defined periods of expected recovery and return to work for common medical conditions and common surgical procedures.
Department advice states: "For the most common health problems, such as back pain and mild to moderate anxiety and depression, advice to stay at work or return to work early is recommended for a better clinical outcome".
The Department of Social Protection is asking GPs to remember that people do better when they are in work, and that excusing them from work for periods of time might put their job at risk.
Social Protection also says being out of work can lead to a deterioration in a patient's health.
They want doctors to encourage patients to think about going back to work earlier than a certificate advises, if they are better.
Doctors who participated in a study carried out before the guidelines were issued said they found the proposals helpful, and that outcomes for patients did improve.
It is being left up to the GP to decide where a patient can best recuperate.