“Our first session of New Member Orientation covered COVID in Congress. Masks, masks, masks,” she tweeted.
“I proudly told my freshman class that masks are oppressive. In GA, we work out, shop, go to restaurants, go to work, and school without masks. My body, my choice,” she said, adding the #FreeYourFace hashtag.
Ms Greene was photographed wearing a mask with the US flag emblazoned on it. At times during orientation, the mask was hanging around her ear and not covering her face.
Madison Cawthorn, another newly-elected Republican, told reporters Ms Greene had a “pretty fiery” exchange over the mask rule with officials.
After her comments were picked up by CNN, Ms Greene took to Twitter to say she had "triggered" the news network.
“Looks like I triggered @mkraju and @CNN during lunch today. Enjoy!” she said in a tweet accompanied by a photo of her watching the network.
The coronavirus has been running through Congress and the White House, with multiple politicians and members of the Trump administration testing positive for the virus in recent months.
President-elect Joe Biden has publicly called on Americans to wear masks, saying it should not be a political issue.
Wearing a mask has become largely politicised in the US, with Mr Trump at times refusing to use one and criticising Mr Biden for doing so.
The US this week passed more than 10 million coronavirus cases. More than 240,000 Americans have died from the virus.