This move will put vice mayor-elect Sara Duterte, 28, his political heir, as the acting mayor.
Rodolfo Rasul, Department of Interior and Local Government regional director said taking a leave is the mayor's constitutional right.
However, he said, all elected officials are "our (public) property" so the mayor should expect a close public scrutiny of his move.
Rasul said that when people elect their leaders, they expect them to give them nothing but the best, including good health.
The mayor issued the announcement in a press conference Monday afternoon.
His daughter Sara, reportedly diagnosed with a kidney ailment, was reported to have undergone an operation, too, and is still in Manila. Duterte said Sara is out of harm's way and is just attending to a personal matter before coming back.
Duterte clarified he didn't want the public to harbor ill thoughts about Sara's foray into the top post. He said he would await inauguration so that at least by that time, somebody has a clear successor as mayor.
Three-term vice mayor Luis Bonguyan ends his three terms on June 30.
The mayor said he has been experiencing pain owing to a spinal problem resulting from a motorcycle accident many years back, aggravated by his latest accident near Bangkerohan public market.
Duterte said the pain was bearable when he was younger "but recently, I am having a hard time moving around," he said.
One of the mayor's aides said he needs a "major orthopedic operation."
Duterte did not name his surgeon but said he was proceeding to Davao Doctors' Hospital after the press conference.
Rasul said the public should welcome Duterte's submission to a surgical operation. He said it shows the mayor is keen on staying fit.
He said who will take charge during the leave should not cause as much problem. "We have well placed rules on succession," he said.
Dabawenyos interviewed by MindaNews did not mind if the city will have two women occupying the top two posts. Reelected councilor Ma. Belen Acosta and councilor-elect Myrna Dalodo Ortiz, are among those seen as top contenders to the vice mayoralty should Sara assume as OIC mayor.
Duterte said he wanted to be operated on as soon as possible bcause "what's bugging me is when it's done, maybe the recuperation will take long.”