At a news conference Saturday evening, Twin Falls Police Chief Matthew Hicks told reporters he could not provide an exact number of people killed or the number of people injured.
There is no active threat to the community, police said.
Police are still working to identify the suspected shooter and his motivation, Hicks said.
The Twin Falls Police Department responded to an "active shooter incident" at the In-and-Out on Blue Lakes Boulevard in Twin Falls on Saturday afternoon.
A large police presence from multiple agencies descended on the scene, Hicks said.
The restaurant is located near a busy shopping area, and police said there were potentially hundreds of people nearby, calling it an "exceptionally chaotic scene."
Police are still interviewing witnesses and asked anyone with information to come forward.
Police urged people to avoid the area to allow emergency crews to work safely.
Idaho Attorney General Raúl Labrador said authorities are searching for the suspect.
"Praying for everyone in Twin Falls as first responders continue searching for the suspect near In-N-Out," Labrador said in a Facebook post.
Roads near the scene, including a bridge in the area, have been closed. Authorities asked the public to use alternate routes and not attempt to enter the area.
The FBI said it is aware of the situation and offering assistance to local law enforcement, according to an agency spokesman.
Twin Falls is a city of more than 56,000 people about 128 miles southeast of Boise.
In a statement on social media, Idaho Gov. Brad Little asked for prayers "as law enforcement and first responders respond to an active shooter situation near In-N-Out."
ABC News contributed to this report.
This is a breaking news story. More details will be added as more information becomes available.