The Scottish Fishermen’s Federation (SFF) has accused ministers of demonstrating “mistrust” in their response to a rare reef being damaged.
In a letter, the SFF said the government’s emergency measures undermine confidence in marine protection.
The flame-shell reef in Loch Carron was damaged when a scallop dredger dragged its gear right through it.
The incident had been investigated by Scottish Natural Heritage (SNH).
It concluded that the damage was consistent with scallop dredging and that there was a “viable” chance of recovery.
On Friday, Environment Secretary Roseanna Cunningham gave Loch Carron emergency protection by designating 16 square kilometres of it a Marine Protected Area (MPA).
But in a letter to Ms Cunningham and Rural Affairs Secretary Fergus Ewing, the federation’s chief executive, Bertie Armstrong, raised concern about the process.
He said five similar reefs were already closed to fishing and that MPAs were designed to protect “examples” of rare sea features, not all of them.
He added that the move was a “de facto statement of mistrust” in the process of Marine Protected Areas.
The letter continued: “You will know that this logical, sequential, evidence-based endeavour is one that we, as directly affected stakeholders, have not only participated in but directly promoted on the international stage as an exemplar for others, balancing well the relevant Scottish government policies of healthy and productive seas.
“Stepping outside the process undermines confidence in a balanced government approach to MPAs.”
On Friday, the environment secretary said the MPA was an emergency measure and that steps would be taken to make it permanent.
Roseanna Cunningham confirmed that the damage was consistent with scallop dredging but that there was a “viable prospect of recovery” for the reef.
The campaign group Open Seas said the move was “too little, too late” and that MPAs should be imposed on even more reefs.