About 75 guests were evacuated from the hotel. No guests, hotel employees or firefighters were injured, Farmington Fire Department Chief Terry Page said. Most of the hotel was reopened Sunday afternoon.
The fire was contained to one room on the second floor of the hotel's west wing.
But smoke and water damaged nearby rooms.
About 60 of the hotel's 192 rooms are closed for repairs because of the fire, said Pam Scott, Red Lion's director of corporate communications.
She said it's too soon to know when those rooms will be reopened.
Scott said the hotel's remaining rooms, restaurant, lounge and meeting room are open and guests stayed in the hotel's two other wings Sunday night.
"The guests were reimbursed for their overnight (Saturday) stay," Scott said.
Battalion Chief Jay Balfour said firefighters began escorting guests back to their rooms to check on their belongings at about noon on Sunday.
Scott said no guests complained of damaged property because of the fire.
Page said the investigation into the cause of the fire is ongoing but investigators have found the fire's sole point of origin in the storage room.
When firefighters arrived shortly before 5 a.m., there was no smoke visible from outside the hotel but it was smoky in the lobby and on the first floor, Page said.
The second and third floors had considerably more smoke in the air.
The Fire Chief credited the hotel's alarm system for waking up all the guests and getting them to safety.
"The hotel recently installed a brand new alarm system and it did exactly what it was supposed to do," Page said. "A fire in a hotel is a pretty significant event. ... History will tell you a hotel fire can be very bad as far as loss of life goes."