Emergency services were called to the Don Bridge at Kintore, in Aberdeenshire, at around 8.35am.
The Grampian Police underwater search unit was sent to the scene along with fire crews and the Scottish Ambulance Service.
It is not known how the tractor ended up in the River Don, which is in heavy spate.
Grampian Fire and Rescue spokesman David Rout said: “The tractor is submerged in water and we can barely see it.
“We have reason to believe that there is one person in the vehicle.”
Police were still trying to establish whether the man had tried to escape from the vehicle himself.
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