The crofter at the centre of the row is Murdo MacLennan, a respected figure in the Western Isles who has been active in crofting for 30 years.
A former building society manager and chief executive of the Western Isles Health Board, he was appointed a commissioner on the old Crofters Commission and served for six years. He was then elected to the new body, the Crofting Commission, earlier this year.
He agreed crofters should live on their crofts or as near to them as possible, and defended his role as commissioner.
But at least six letters from crofters are understood to have been received by the new commission complaining that Mr MacLennan, who adjudicates on absenteeism, is an absentee, and questioning why he was allowed to stand for election.
The Crofting Commission took over from the Crofters Commission in April, with six of its nine commissioners directly elected for the first time.
One of its main aims is to promote croft occupancy and active use. It requires crofters to live within 20 miles of crofts or be deemed absentees.
The commission can impose a tenant on a croft owned or rented by an absentee. There are currently around 1700 absentees.
Last night, Mr MacLennan defended his role on the body. He said: "I live on my family's croft at Aignis in the Point area of Lewis. But I also inherited two other croft tenancies – one in Cliasmol on Harris in 1987 which is over 50 miles away, which takes me an hour from my home, and another on the uninhabited island of Scarp off Harris, in 2005.
"There are only four active crofters with crofts on Scarp and obviously none of us now stays on the island. But we work hard just to make sure there is still some crofting activity on the island."
He has approached the North Harris Trust, the community-led landowner, to see if there was demand locally to take over the tenancy at Cliasmol.
He said the old commission investigated his absenteeism in 2011, but he had letters of support proving he was an active crofter in the North Harris area, so the commission agreed to review the case in 2016.
He confirmed he was still involved with absentee cases. "The chairman of the old Crofters Commission took the view that I had been appointed to act as a commissioner on a regulatory body so should sit in on meetings concerning cases of absenteeism."
It was the same on the new body, he said: "When I stood for election to the new commission earlier this year, all my election literature made clear that I was crofting in both Lewis and Harris. So people knew very well that I lived in Lewis and expressed their support for me very clearly in the ballot box."
The commission's own minutes show the issue was raised at a meeting in July, by another commissioner, Colin Kennedy, who said a commissioner who was an absentee should not take part in decisions on occupancy, as it could cause a perception of impropriety.
Mr Kennedy, from Coll, declined to comment, but a spokeswoman for the Crofting Commission confirmed Mr MacLennan was deemed an absentee.
On whether he should have been allowed to stand, she said: "The commission is aware that there may be an ambiguity within the interpretation of the regulations and is looking into this for the future."
There are 12,000 crofters on 18,027 crofts. More than 300 absentee cases were resolved over the past two years following contact from the Crofting Commission. A total of 29 tenancies were terminated.