Two fire engines from Deeside and Flint were called to the Wales-based mill at 1.45pm, and the fire became under control a few hours later.
A spokeswoman for North Wales Fire and Rescue said no one was hurt in the incident.
A UPM spokesman said production was up and running fairly shortly afterwards.
He said: "The cause is to be provided, but it was a small fire which required additional assistance.
"UPM Shotton's fire crews are trained by fire and rescue to deal with these incidents and all emergency procedures were followed."