In an internal message to FBI employees, FBI Director James Comey says he's confident the FBI made the right decisions during a challenging year, one that included a "contentious election."

"I would be lying if I said the external criticism doesn't bother me at all, but the truth is, it doesn't bother me much because of the way we made decisions. At every turn last year, we were faced with choosing among bad options and making decisions we knew would bring a torrent of criticism."

FBI Director James Comey is sworn in before testifying before a House Judiciary Committee hearing on "Oversight of the Federal Bureau of Investigation" on Capitol Hill in Washington, Sept. 28. JOSHUA ROBERTS / Reuters

His comments came in an annual New Year message, sent Tuesday to FBI employees.

"People often ask me what we should do to respond to those who have questions or concerns about the FBI in the wake of a contentious election cycle. 'Do great work' is my answer," he said. "When you know you have made decisions thoughtfully and consistent with your values, it is freeing, in a way."

In the nearly 3,000 word message, Comey mentioned the probe into former secretary of state Hillary Clinton's use of a private email server only once, listing it as one example of events that made 2016 "a challenging year." The list also included the Orlando nightclub shooting and the standoff at an Oregon wildlife refuge.

"As it always is, our work was subject to a fair amount of second-guessing. We try to stare hard at our own work, take feedback that is thoughtful, and always week to be better."

Among accomplishments, Comey mentioned the hiring of 3,059 new employees, with another 2,500 expected in 2017 — which would bring the FBI to its fully authorized strength — an overhaul of the firearms background check system, and improvements to the FBI's management of computer systems used in investigations.