In particular, Donnie Ross, 77, cited Scottish Natural Heritage's (SNH) designation of croft land for environmental protection as a reason for his resignation.
A keystone of the Scottish Government's crofting reform legislation was that crofters would stand for election to the regulatory body.
Six were elected and joined three commissioners on the new Crofting Commission appointed by ministers.
They replaced the old Crofters Commission which was appointed by ministers.
Mr Ross was elected to represent the East Highlands constituency for East Sutherland, Easter Ross, East Inverness and Moray.
Since his election he has been a persistent critic of SNH, and has now said he is standing down.
He said: "The grounds that I have given are that the government, whichever one it was, deceitfully led people like me and the crofters who voted for me, into believing that this new Crofting Commission would be a body to look after crofters and their needs and rights. It is absolutely not.
"It is a purely regulatory body that is so tied up with this dictatorial government's rules that even if it wanted to, it could not become more crofter-friendly or representative of crofters' needs and rights. It is not even allowed to criticise other government bodies like SNH."
He said he firmly believed the real reason the Committee of Inquiry into Crofting had recommended the setting up of the new commission, ".. was for no other reason than to make crofting ever more environmentally-controlled." He said an example of this was SNH being allowed to put designations on 64% of local townships' hill grazings.
A Scottish Government spokesman said: "Ministers thank Mr Ross for his contribution during his time as a Crofting Commissioner and will now proceed with filling the vacancy in accordance with the legislation." He said the Commissioner for Public Appointments was being approached for guidance.
An SNH spokesman said it would not be responding to Mr Ross' comments.