His team, Dimension Data, confirmed he has been told to rest up, but SunSport understands it is not long-term — and he hopes to be back as soon as possible.
The Manx Missile, 33, rode the Tour de France last month but missed the cut-off during a mountain stage.
But he today revealed he has been trying to train while carrying Epstein-Barr virus, which causes glandular fever.
The Isle of Man speedster had previously been diagnosed with the energy-sapping virus last year, but he is not planning on being off the bike long-term.
Cavendish said: "This season I’ve not felt physically myself and despite showing good numbers on the bike I have felt that there’s been something not right.
"Given this and on the back of these medical results, I’m glad to now finally have some clarity as to why I haven’t been able to perform at my optimum level during this time.
"Having received expert medical advice as a result of the findings I’ve been advised to take a period of total rest in order to fully recover.
"I’m now looking forward to taking the time necessary in order to get back to 100 per cent fitness before then returning to racing again at peak physical condition.
"I’d like to thank everyone for the incredible support I’ve received and I look forward to seeing you all out on the road again soon."
Cavendish last rode at Prudential RideLondon a month ago and bowed out of the Tour de France the week before — after failing to make the time cut, along with a host of other sprint specialists in brutal mountain stages.
The 30-time Tour stage winner was given plaudits for finishing the stage though, despite knowing he would be eliminated, such is the esteem in which he holds the race.
His wife Peta exclusively revealed to The Sun how he had left her with their five-day-old child Casper to prepare for the Tour.
She said: "Mark had missed a time cut in the Tour de France, meaning he was out of the race and would be coming home two weeks early.
"He was devastated. He had left to continue his preparations for that one race when our new baby was just five days old.
"Mark was away for more than a month, but it seemed like the sacrifice was worth nothing.
"Why are we having such bad luck?"
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