On Tuesday, the Hartford, Connecticut-based company also reported profits and sales that beat analysts' expectations. In addition, it raised its forecast for 2014.

Bertolini said medical costs were "hard to predict" because small group and individual policy holders are gearing up for changes in Obamacare, he said. However, he expects Aetna will meet annual guidance.

The CEO has criticized Obamacare in the past, saying it is not an affordable product for many people and doesn't fix the underlying problems causing high health-care costs.

It will be "a long way" before Obamacare settles down and "more healthier enrollees come into the program," he said Tuesday.

There will also be some confusion as participants have to re-enroll for the first time.

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"We want it go smoothly and we're working with the administration and with CMS [Centers for Medicare & Medicaid Services] to make it go smoothly," he said. "But I think folks are going to be a little confused about how to access the system."

That said, for the first three-quarters of the year, the on-exchange membership has been profitable because operating costs are lower, he noted. A return on capital, however, will take some time because of health-care costs, he said.

Bertolini anticipates rate increases will be in the mid- to low-teens, "in the middle of the pack."

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Rising health-care costs not a trend: Aetna CEO