Lee concurs and, during implementation periods, will turn to consultants if he can't find candidates who are familiar with software from health IT vendor Epic Systems.

"There's not an endless supply of Epic-certified analysts out there in the universe," he said. "We have higher needs during implementation. We won't have all those analysts on staff. We will use consultants to keep a stable of trained Epic consultants."

To meet the worker demand, the federal government allocated approximately $120 million in grants to community colleges for health IT training. Experts anticipate that these programs will pay off in a few years since hospitals need skilled workers now in order to meet immediate deadlines and some organizations want more seasoned graduates.

"Health care systems don't have time to get someone up to speed in six months" with how the incentive program is structured, Marx said.

"CIOs feel like people coming out of the programs are not perfectly aligned with their needs," he continued. "They needed someone with a clinical background."