"I'm disappointed in that decision for them not to be here," Harbaugh said Tuesday, according to CSN Bay Area.
Both players have missed the entirety of the team's offseason program. Davis forfeited a $200,000 workout bonus; Boone gave up his $50,000 workout bonus.
"As a voluntary segment to the offseason and we appreciate those guys volunteering to make the team better," Harbaugh said. "Now, it's mandatory and wish they could've ... (it's) not the decision I envision being the 49er way."
Davis and Boone will each lose about $70,000 if they sit out the entirety of the team's three-day mandatory minicamp, according to the terms of the NFL's collective bargaining agreement.
Longtime Niners beat writer Matt Maiocco tweeted that Harbaugh's comments "might be the sharpest rebuke" the coach has directed at his players during his tenure. Harbaugh must be steaming to let the media know where he stands.