Dr Anne McCloskey expressed concerns about young people being given the vaccine.
In a video posted online on Sunday, she made a number of claims including that there is not enough evidence it is safe for young people to be vaccinated.
The Health and Social Care Board (HSCB) ordered an investigation after receiving complaints about the comments.
On Tuesday, the HSCB confirmed it has suspended Dr McCloskey as a precautionary measure while it investigates.
“Suspension is not an automatic occurrence when undertaking an investigation but may be necessary where there are concerns regarding patient safety and in the public interest,” a spokesperson said.
“Dr McCloskey is not free to work for HSC organisations during her suspension.”
In an interview with the BBC, Dr McCloskey said she stands by her comments.