"First of all, I don't know where to start," Na said at the Shriners Hospitals for Children Open, according to Golf Channel's Nick Menta.
"Yes, what he did was wrong," he continued. "Should he be fined? Yes. (But) three years is ridiculous."
Na, who was born in South Korea, called himself a "big brother" to Kim, with their relationship growing since the two played on the PGA Tour together in 2011.
Na recently spoke with the disheartened golfer, who has apologized for his actions.
"He's depressed. I mean, I can hear it in his voice," Na added. "I said, 'You know what? I know you're going through a rough time. Be good to your wife. I am sure it's hard for her.'"
Kim's wife is pregnant with the couple's first child.
The 29-year-old won the Daegu Gyeongbuk Open after his obscene gesture on the 16th hole in the final round. He was leading the Korean Tour in earnings at the time of the ban, and Kim was set to qualify for The CJ Cup on the PGA Tour. He was also in position to earn playing status on the European Tour.
"You can't take a man's job away for three years for one incident. Everybody makes mistakes," Na said. "Like I said, if this was (his) fifth or sixth offense, I get it. But when you have no offenses and have had good behavior, you're a good guy, people like him, you can't do that to a person."
Na has tried to help by reaching out to those in power in Korea. He's also provided Kim with PGA Tour contacts for possible playing opportunities.
Na's caddie wore a "Free Bio Kim" hat on Thursday at the Shriners Open.
Kim won't appeal the three-year suspension. He believes appealing would suggest his apology is not sincere, according to ESPN's Bob Harig.