Can an employee opt out of withholding on a bonus?

Q: It’s likely that later this year, one employee will receive a bonus that will boost his supplemental pay to more than $1 million. In anticipation of that, his accountant has informed us that we don’t need to withhold federal income taxes at the 39.6% rate; the employee will pay the tax on his 2015 Form 1040, instead. Is that right—it sounds fishy to us?