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It says if organisations need proof that people are unwell, they could require a medical certificate after seven days of illness rather than the usual three.
Royal New Zealand College of General Practitioners medical director Bryan Betty said doctors often mentioned the problem.
"We have a situation at the moment where the system is essentially at capacity in terms of the winter illnesses we have such as influenza, Covid, RSV, and certainly it's an additional burden that at times is probably unnecessary and it's one that GPs reflect back to me quite frequently on."
He said schools and employers should think about waiving the requirement for certificates or at least extending the time period for which they are required.
"We've been putting out the messaging as a health system that if you are sick or unwell with the flu or flu-like illness you should be at home so you don't spread it.
"In fact for Covid it's mandatory to be home for seven days, so I wonder if there could be some thought given to if we are going to maintain the certificates whether we increase the timeframe to seven days," Dr Betty said.
Schools had been hard hit by illness this year with teachers claiming twice as many sick days as at the same time in 2019.
Principals' Federation president Cherie Taylor-Patel said most schools were not requiring certificates unless they had doubts about the student or staff member concerned.
"There are some instances people might be wondering if they do need to ask for a medical certificate if there is an issue with people not coming back that are well, but in most instances people do want to come back to school," she said.
Business New Zealand employment relations policy manager Paul MacKay said employers had a legal right to ask for a medical certificate after three days of illness but they understood that doctors were under pressure.
"Most employers would sympathise with the plight of GPs who are seeing so many people now with Covid, with RSV, with flu and so on that there would be a rational or a reasonable conversation to be had about taking a more lenient stance with medical certificates," he said.
MacKay said it was inevitable some people would use sick leave when they were not sick but businesses were not reporting a particular problem with that and they did not want people coming to work and spreading viruses.
"We've got a bit of a risk in both directions and I think that requires a mature and reasonable conversation at every level to say let's be realistic here, I won't require certificates as a matter of course because for a start it's going to cost a lot of money for an employer to send all of their employees to a doctor. At the same time employees need to know they need to be responsible and stay away if they are sick," he said.
MacKay said employers also had to accept that it might not be possible for their employees to get an appointment with a GP.