Tim Passmore said claims Douglas Paxton's continued absence was linked to poor relations between the pair were "a load of old tosh".
He said: "There has definitely not been a bust-up. [I] 120% deny that."
He would not elaborate on Mr Paxton's illness. The BBC understands his condition is not life-threatening.
Mr Paxton, 49, started the Â£133,845-a-year-job in March 2013, having been the only person to apply for the role.
Last month, Conservative PCC Mr Passmore said Mr Paxton would be off "for the foreseeable future" and that Deputy Chief Constable Gareth Wilson would be standing in.
Speaking to BBC Look East, Mr Passmore said he was "really surprised" when he heard Mr Paxton was off work.
"We were at the Christmas lunch in the canteen and he said a few words, we had a chat, I said a few words and the next thing I knew he was off," he said.
In a separate interview with BBC Radio Suffolk's Mark Murphy, Mr Passmore said he was aware of the extent of Mr Paxton's illness, but said he had been "asked not to divulge people's personal medical details".
Mr Passmore said he had disagreed with Mr Paxton about certain issues, including the ultimately doomed proposed merger of Suffolk and Norfolk's control rooms.
"My role as PCC is to hold the constabulary to account via the chief constable and when we have robust conversations, which we do, it's very, very important we explore all the issues in great detail," he said.
"It's not some sort of lovey-dovey relationship."
Suffolk Police declined to comment.
Suffolk's police and crime commissioner has denied having a "bust-up" with the force's chief constable, who has been off sick since December.