The Australian radio and television personality, who presents the station's breakfast show with Jackie O, has regularly had days off due to illness in the last few months. Although still the most popular programme, listener ratings have now slipped 1.3% from 11.3% to 10% audience share.
2DayFM's content director Derek Bargwanna told The Daily Telegraph: "Kyle and Jackie were both away at separate times during the survey period due to illness and we thank the audience for continuing to choose 2DayFM as their first choice.
"While it's not ideal to have Kyle and Jackie off, we've got great stars on hand to fill their big shoes. Sophie Monk, Mel B [and] Brian McFadden have all helped out when needed."
Radio station Nova registered the biggest loss of the past three months with its audience figures dropping from 7.2% to 5.7%.
Sandilands was reportedly told in 2008 that he should quit smoking and drinking caffeinated drinks or risk dying young. In March, he was rushed to a Sydney hospital while filming for Australia's Got Talent due to high blood pressure. The following month, he took time off from his radio show because he had "no voice".
He has since reportedly embarked on a fitness regime in a bid to lose weight.