"Compared to 2015, the stock numbers in 2016 were below the recommended level and at the point where action is now needed to increase the number of fish of breeding age", said Bernadette Clarke, Good Fish Guide manager.
The Marine Stewardship Council (MSC) and the Marine Conservation Society (MCS) appear to be fundamentally opposed over the sustainability rating of Scottish haddock.
But British haddock from three North Sea and West of Scotland fisheries has now been removed from the "green" list of sustainable "fish to eat", which is compiled by the Marine Conservation Society.
Other updates to the Guide include improved ratings for nephrops (scampi) fisheries in the west of Scotland, Clyde and Jura catch areas, though the MCS says the fish is still "some way off" being sustainable.
They have been downgraded because stock numbers in 2016 were below the recommended level and action was needed to increase the number of fish of breeding age, the MCS said.
As a group, tuna are one of the UK's five most popular fish to eat, and the United Kingdom is the second-largest importer of tuna in the world.
However, Scottish fishermen's representatives told the Guardian the move as "dressing advocacy up as science".
Campaigners are urging consumers to seek "green-certified" haddock, which are caught in the northeast Arctic and Iceland, when buying this species or buy other fish on the green list such as coley, mackerel and hake.
SFF chief executive Bertie Armstrong said: "The MCS has completely misunderstood the position as far as haddock stocks are concerned and should withdraw its utterly misleading comments". "We have gone to enormous lengths to maintain fishing stocks, including haddock", he said.
Haddock from the North Sea and the west of Scotland have been taken off a list of sustainable "fish to eat".
North Sea haddock previously had a better rating than North Sea cod but the latter is recovering while the haddock stock is at "very high risk", according to the latest scientific assessment.
"I'll be choosing MSC labelled Scottish haddock tonight for my fish and chip supper knowing that it's been caught by responsible fishermen with sustainable management that's been checked and monitored by the world's most rigorous scientific test of sustainability".
New additions to the Guide include American lobster (rated two), which can retail at under £10 in United Kingdom supermarkets at Christmas.