That estimate does not take into account those workers who need to stay home to care for a sick family member.

"We're predicting about 11 million Americans will fall ill over the flu season and that's going to cost employers over $9 billion in wages being paid to employees that are staying home sick," Andy Challenger, the firm's vice president, told CNBC's " Closing Bell " on Friday.

With a nasty flu season underway across the country, businesses can expect to see billions of dollars in lost productivity, according to global outplacement consultancy Challenger, Gray & Christmas.

Emergency room nurse Christine Bauer treats Joshua Lagade of Vista, California, for the flu as his girlfriend Mayra Mora looks on in the emergency room at Palomar Medical Center in Escondido, California, January 18, 2018.

According to the Centers for Disease Control, the flu is now widespread across the continental United States.

The predominant strain, H3N2, isn't well prevented by the flu vaccine.

"We've got a dominant virus out there that causes more severe disease, causes more complications particularly among older persons and the very young," said Dr. William Schaffner, professor at Vanderbilt University Medical Center.

Challenger said it's important that workers don't try to tough it out and go into the office and that employers discourage sick employees from coming in. Limiting meetings and expanding remote work options are two ways to help prevent the spread of the illness, he noted.

"It's better to make sure an entire department doesn't fall ill and cost the company a lot of money over the flu season," Challenger said.

As for when to return to the office, Schaffner said, "After you've started to get better, two, three days after the onset of disease, if you're adult you can come on back to work."

If the worker has a fever, the CDC recommends staying home for at least 24 hours until the fever subsides.

— CNBC's Meg Tirrell and Reuters contributed to this report.