Rapoza said he couldn't speak to why the employee wasn't co-operating with federal investigators.
"With regard to our internal investigations, he has taken the position that he provided a written statement shortly after the incident, and doesn't need to speak to investigators because he has nothing to add," Mr Rapoza said in an email.
The agency has not identified the employee. He continues to work at the agency though has been reassigned to a section where he doesn't have access to the warning system.
FCC spokeswoman Tina Pelkey, when asked what reason the employee had given for not co-operating with its probe, said the commission had no further comment.
The alert sent to mobile phone, TV and radio stations in Hawaii on January 13 caused widespread panic and confusion. The problem was compounded by the lengthy amount of time — 38 minutes — it took the emergency management agency to send a corrected alert.
After the incident, the agency began requiring two people to sign off on the transmission of tests and alerts.
It drafted a correction that it will be able to send immediately if someone accidentally sends a missile alert in the future.
US Senator Brian Schatz, a Democrat from Hawaii, told the committee he was introducing legislation that would make it clear the authority to issue missile alerts rested with the US defence department and homeland security, not with state and local governments.
"It is increasingly clear to me that if we get all 50 states and all the territories and 3007 counties across the country participating in this program, the likelihood of another mistaken missile alert as a result of human or bureaucratic error is not zero," Mr Schatz said.