Obamacare monopoly would be 'very sad': Athenahealth CEO

Athenaheath CEO on improving Obamacare

As the White House looks to make sure insurance companies don't lose money on Obamacare, such a move would be a slip toward making the government the only real player in health care, Athenahealth Chairman and CEO Jonathan Bush told CNBC on Wednesday.

"[That] would be very sad for all of us," said Bush, whose company makes Internet cloud-based solutions for medical billing and practice management.

In hundreds of pages of new regulations released last week, the Obama administration has quietly adjusted key provisions in the president's health-care law, according to an analysis by the Los Angeles Times. The moves would potentially make billions of additional taxpayer dollars available to insurance companies if they lose money, the paper said.

Bush has not been a huge fan of Obamacare. "What the administration should have done is, of course, let those players that are in the [health exchanges] choose a wider range of benefits than the ones the government makes them offer—so that different people could buy different things," he said in Wednesday's interview with CNBC's "Squawk Box."

Many critics have called for more a la carte choices on what's covered and what's not in order to avoid paying for unnecessary coverage.

'Where Does It Hurt'

Athenaheath CEO: 'Where does it hurt'

Bush has lots of ideas on how to overhaul health care and he's out with a new book on the subject called, "Where Does It Hurt—An Entrepreneur's Guide to Fixing Health Care."

He told CNBC that health-care companies need to redefine their markets just as Apple did. "The example that we all know is Microsoft versus Apple. Apple wakes up one day and says, 'Wait a minute, I don't want to just sell computers. I want to sell computing.' So the iPod and all these things broke open the market for computing. They're still smaller than Microsoft on laptops, but they're way bigger because they've redefined the market."

As CEO of a company that makes money in the health-care industry, Bush addressed critics who say he's written a book as a promotion vehicle.

"The health-care information neighborhood would be a lot better with a 'second Starbucks,' just like all neighborhoods. It doesn't have to be in Athenahealth. There has to be health-care cloud in the marketplace, which is barely covered in the book."

Earlier this month, Bush appeared on "Squawk Box" to defend Athenahealth, after hedge fund manager David Einhorn made a case for shorting the stock.

Bush said he believes Athenahealth is a "$1,000 a share stock," but did not put a timetable on such a move.

Read MoreHey, Einhorn? Athenahealth a $1,000 stock, CEO says

Einhorn, co-founder of Greenlight Capital, called Athenahealth a "bubble" stock that could fall 80 percent or more from its peak share price of more than $204 in March. He also said the company's potential products are being overvalued.

Athenahealth shares closed Tuesday at about $114.

—By CNBC's Matthew J. Belvedere