No matter that Whole Foods already provides benefits to team members who work at least 30 hours. The problem, Mackey explained, is that the type of benefit plans the government will likely mandate, will require more benefit coverage than he provides now. (Read More: Will Obamacare Spark the Next Tech Boom?)
The Health and Human Services Department is expected to finalize benefit coverage requirements later this spring, but Mackey said they are sure to raise costs.
Mackey told CNBC that he could be wrong about that, but doubts it. (Read More: Obamacare Is Here to Stay. Now What?)
"Could it work out? Sure," he said. "It's been my experience, though, that bureaucracies are not very flexible and they don't have great outcomes."
—By Bertha Coombs; Follow her on Twitter: