Firefighters worked through the night against a blaze that erupted Sunday morning and sent a huge plume of smoke over parts of the region.
Five helicopters and eight air tankers dropped fire suppression chemicals and as 300 firefighters worked feverishly to contain the blaze.
A federal management team was taking over direction of the effort Monday, a move that will expand access to firefighting resources.
There have been no reports of serious injuries or damage to buildings in this blaze and a smaller one sparked Saturday that also spurred evacuations across town.
The city and Coconino County declared states of emergency, and officials closed U.S. 89, a key route to Grand Canyon National Park about 75 miles to the north.
Strong winds fueled the flames. "The higher winds definitely played a key role in the extreme behavior of the fire today and it will continue tomorrow," said city spokeswoman Stephanie Smith Sunday night.
Residents of hundreds of homes were urged to evacuate because of the blaze, dubbed the Schultz fire. Many heeded the call but their numbers were unclear. Others watched from their properties as bright red and orange flames climbed over a mountain behind a cloud of towering smoke.
Jennifer Whitehair was having lunch in town when she heard her neighborhood was being evacuated. She rushed home, grabbed some important possessions and then sat at a nearby gas station and watched as flames made their way over a mountain and within several hundred feet of her home.
"When something like this happens, it makes you thankful for the things you do have," she said. "The material things seem less important, although in one sense it's your life."
Fire spokesman Eric Neitzel said the fire had moderated somewhat by midnight but was still strong. He said that earlier in the evening, flames came within 500 yards of a scattering of homes beneath the mountain, spurring firefighters to build a containment line.
Meanwhile, in the southeastern end of town, evacuation orders for a separate fire the emerged Saturday were lifted after officials reported it 25 percent contained. Residents of the 116 homes evacuated because of the blaze were being allowed to return after crews established a containment perimeter.
A California man was arrested on suspicion of starting the smaller blazed, called the Hardy fire, by leaving behind hot coals at a campsite in a wooded area.
The American Red Cross set up a shelter for displaced residents at a Flagstaff middle school but few were staying overnight.
Kyle Lathrop didn't plan to remain at a shelter.
He had been planting flowers in his backyard and initially thought the fire would bypass his area. But when he saw a neighbor loading horses and talked to others, he said he knew it was time to go. He packed up some important possessions, his 7-year-old dog Madline, and headed to a shelter to check in but planned to stay elsewhere.
"That's always a risk, part of the pleasure of living in the semi-rural area," he said. "You get the view, but you have the risk (of fire)."
Fires also had crews busy Sunday near Williams, Ariz., and in Colorado and New Mexico.
Fire danger is considered high to extreme in Arizona, which has seen two wildfires burn more than 3,000 acres each in the last month.
Relief isn't expected until next month, when summer monsoons generally start bringing rain to the region.
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Associated Press writer Susan Montoya Bryan in Albuquerque, N.M., contributed to this report.
