Joasia Zakrzewski finished third in the 2023 GB Ultras Manchester to Liverpool 50-mile race - but is thought to have travelled by car for 2.5 miles.
The 47-year-old GP, from Dumfries, is understood to have been tracked on GPX mapping data covering a mile of the race in just one minute 40 seconds.
A friend said Ms Zakrzewski had felt sick and was sorry for any upset.
The matter has been referred to UK Athletics.
Wayne Drinkwater, the director of the GB Ultras race, said that after the ultramarathon he received information that a runner had gained an "unsporting, competitive advantage during a section of the event".
He said: "The issue has been investigated and, having reviewed the data from our race tracking system, GPX data, statements provided from our event team, other competitors and from the participant herself, we can confirm that a runner has now been disqualified from the event having taken vehicle transport during part of the route."
Mr Drinkwater said a report of the disqualification had been submitted to the Trail Running Association, which provides the licence for the event and is an associate member of UK Athletics.
"The matter is now with the TRA and, in turn, UK Athletics (UKA) as the regulatory bodies," he said.
Third place in the race, which was held on 7 April, has now been awarded to Mel Sykes.
Scottish Athletics chairman David Ovens said: "It is very disappointing to hear this, given Joasia's had such a successful period over the last few years.
"I hope she can put this behind her and that there is an innocent explanation and she can resume her successful career."
Adrian Stott, a running friend who has been in contact with Ms Zakrzewski since the event, said she had arrived the night before the race after travelling for 48 hours from Australia.
"The race didn't go to plan. She said she was feeling sick and tired on the race and wanted to drop out," he said.
"She has cooperated fully with the race organisers' investigations, giving them a full account of what happened.
"She genuinely feels sorry for any upset caused."
And he added: "Joasia has been a great ambassador for British sport and has inspired so many women to run and achieve their goals."
In February, at the Taipei Ultramarathon in Taiwan, Ms Zakrzewski won the 48-hour race outright - setting a world record across 255 miles (411.5 km).
Racing for Great Britain in the IAU World 100km Championships, she won individual silver in 2011 and bronze in 2014 and 2015.
She also represented Team Scotland in the marathon at the Glasgow 2014 Commonwealth Games.
In 2020, aged 44, she won a 24-hour event in Australia with a distance of 236.561km.
She has set a number of records including the Scottish 24-hour record, the British 200k and the Scottish 100 miles record.