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The blaze, near Waipiata-Kokonga Rd, about 10km southeast of Ranfurly, was one of two believed to have been sparked by lightning on Wednesday night.
A smaller fire in Four Mile Rd, near Hyde, was contained by yesterday morning but the main blaze raged on, fanned by strong northwesterly winds, gusting to 80kmh.
Speaking at a paddock-based command centre about noon yesterday, Waitaki deputy principal rural fire officer and incident controller Mike Harrison said strong winds were making the work difficult, spreading the perimeter of the fire to about 300ha at its peak.
"That makes it really hard for our chopper pilots, and they're doing a sterling job up there.
"But it also makes it really hard for our ground crews as well, so we're keeping a really close eye on the weather."
The fire danger in the area was extreme and a total fire ban was in place.
Mr Harrison said the dry tussock, grass and matagouri was excellent fuel and added to the challenge.
About 60 crew including pilots, firefighters and other support staff were involved in tackling the blaze.
Police from around Otago bolstered the ranks of local officers and door-knocked residents from Waipiata to Hyde, who were warned to be ready to evacuate at short notice if required.
The section of the Otago Central Rail Trail near the blaze was closed yesterday.
Kokonga Lodge owner Alexis Siemans said she and 10 guests retreated to accommodation in Hyde.
By late afternoon, a southerly had brought lighter winds, cooler temperatures and much-needed rain.
Fire crews wrestled back control of the blaze to within the perimeter, and by 4pm Fire and Emergency New Zealand spokeswoman Zelda Jordan said crews were in the "mopping up" phase.