OMM organisers had appealed for participants who had already left the area to get in touch and let them know they were safe.
As the hunt progressed, the number of OMM competitors who were unaccounted for fell rapidly to 42, and then 14.
By 1300 GMT an RAF rescue helicopter was searching for the final six missing racers, comprising three teams.
The OMM was abandoned at about midday on Saturday after being hit by some of the worst weather in its 41-year history.
It has taken place every year since 1968 at locations across northern England, north Wales and Scotland.
According to the race website, the end of October is chosen "to allow weather to enhance the challenge".
There are various courses ranging between 40 km (24.8 miles) and 80 km in length, with an ascent of up to 3000m.
Extreme conditions on the mountains and severe flooding made it difficult to get the message to competitors scattered across the hills, often with no means of communication.
Mountain rescue teams searched the hills until after dark on Saturday.
RAF Flt Lt Curly Crawford earlier said a helicopter crew had airlifted five runners and two mountain rescue volunteers to safety.
"A female had been washed into a river by the rains, and obviously [was] in grave danger of being washed away," he told the BBC.
"Fortunately she'd been recovered by fellow runners but was severely injured and suffering from hypothermia."
Cumbria County Council said it opened a reception centre overnight at Cockermouth school and worked with volunteers from the Red Cross and local supermarkets to shelter and feed racers.
Authorities are currently working to reunite competitors, who were competing in teams of two, with their vehicles, and the council is providing transportation.
Police said the B5289 between Seathwaite and Keswick is now passable with care and police are still ascertaining which other local roads are open.
One competitor, Rob Darrington, said at times the high winds and rain had felt as though it was "blowing needles into your face".
Another competitor Jules Carter defended the event.
"Obviously the flooding just took things a step too far this time unfortunately," he said.
Overnight, 300 runners sheltered in Honister slate mine, which has seen 1ft (40cm) of rain fall since Thursday, according to the Environment Agency.
Mine manager Mark Weir was critical of organisers who had "overwhelmed the emergency service" by allowing the race to go ahead.
But OMM organisers defended their decision to stage the event.
An article on the its website on Saturday said: "The idea of self-reliance isn't a popular one in this day and age, so the fact that 900 people are said to be unaccounted for is being presented with the implication they are lost and in trouble - which is not the case."
About 400 runners stayed at Gatesgarth farm, while Glaramara Centre and Cockermouth Sheep and Wool Centre gave refuge to dozens of runners.
It is understood casualties were admitted to the Mary Hewetson Cottage Hospital, in Keswick, and later moved to Cumberland Infirmary, in Carlisle, and West Cumberland Hospital, in Whitehaven, for treatment.
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