TODAY marks another jerk of the clock hand for fishermen in Scotland's white fish and shellfish industries.

They now have exactly two months to upgrade their trawler nets to meet new Scottish Government regulations that come into force on June 1.

The changes, at least to this non-technical mind, involve attaching special panels to nets to ensure that unwanted species of fish can escape back into the water painlessly during a trawl. According to an enthusiastic Mike Park, the chief executive of the Scottish White Fish Producers Association, trials suggest this will reduce cod deaths by 80% and smaller fish by 60% to 70%.

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If this bears out, it will make a huge difference to the quantities of fish that survive Scottish trawling. The numbers of fish that get dumped at sea because they are not permitted under EU quotas – dubbed "discards" – are not far behind the tonnages that are landed back at shore for processing.

Particularly in relation to cod, the improved nets are raising hopes that the fishermen's nightmare years could soon be over. The species exploded in numbers in the 1970s along with other whitefish for reasons that nobody has ever explained, conveniently coming at a time when herring was dwindling from over-fishing.

Captain Birds Eye usurped the great British kipper on dinner tables around the country as white fishing went into overdrive, spurred by generous public subsidies. By the mid-1990s there were 240 British whitefish vessels, most of them Scottish, with crews numbering nearly 2000.

Then scientists started warning that cod stocks were falling off a cliff from over-fishing. Regulation and vessel numbers did not respond quickly enough, which led to tough quotas being imposed in the early 2000s to allow the species to recover. When this didn't make enough of a difference, the authorities started reducing sea days permitted per vessel per year in 2008.

With the number of vessels and crew now down to 120 and 700 respectively, the industry is worth just £20 million a year – only sixth highest among the species of seafish and around one-twentieth of salmon farming. Little wonder that the cod fishermen have to content themselves with prices that have pushed the species to the top end of gourmet restaurant menus.

The sea days per vessel for this year are down to 90 and still the screws are being tightened. With 80 days in prospect for next year, everyone is hoping that the eco-friendly nets will cut the numbers of cod discards and boost the species again. It is also hoped that it will bring back the various supermarket multiples to the North Sea that have abandoned it in recent years over environmentalist pressure.

Park says the restrictions take some of the shine off the one boon for white fishermen in 2012, which is that the haddock quota is being bumped up by around 15%.

"When you are restricted to a certain number of days, you have to look at opportunities where you can hit the stocks fast and hard. You go where the fish are more abundant," he says.

They can get the fish, in other words, but only with a punishing effort that will up the number of discards (making the new nets even more important). Even then they have to get the haddock on the market without offsetting any gains by allowing prices to drop too much. Only then will they add to the value of a fish that at £30m is still a long way behind leaders mackerel, which have become latter day silver darlings, and nephrops (the catch-all for langoustine, scampi and prawns).

There is a strict divide between the fishing of whitefish, which are trawled from the seabed; and pelagic fish like mackerel, herring and whiting, which are caught from nets in the middle of the water. Mackerel is worth well over £100m, with most of it exported outside the EU to countries including Japan and Russia. In 2010, Scotland's 135,000-tonne mackerel haul was divided between the 28 ships licensed to catch them, most of them owned by family businesses in the northern isles and northeast Scotland. The fish swim in such abundant shoals that this big tonnage can be caught within the eight weeks permitted each year, but although mackerel takes much less effort to get out of the water they are less profitable pound for pound on the markets.

Yet this weekend sees a worrying development for the roughly 300 fishermen employed in this segment. Mackerel is losing its sustainable fishing accreditation from the Marine Stewardship Council. This affects not just Scotland but all eight countries that fish for the species in the North Atlantic.

The reason is that for the fourth year in a row, the European mackerel tonnage is going to be way beyond what scientists recommend: 870,000 tonnes forecast to be caught against about 640,000 seen as sustainable. Behind this lies a bitter international battle for control of mackerel fishing that has no end in sight. The perpetrator, at least from a UK point of view, is Iceland, our old opponent in the Cod Wars of the 1950s and 1970s, whose fishermen started catching the fish in the mid-2000s when it began appearing in their waters.

The fish moved there to feed either because water temperatures rose or because the species had become so over-populated that they spread out. Iceland's growing catch chafed at first, but caused serious ructions after it rocketed to 112,000 tonnes in 2008 amid barbs that the country was trying to sort out its balance of payments in the wake of its banking collapse. Mackerel's EU quotas would now be exceeded unless other countries pulled back.

Instead, the tiny Faroe Islands threw another spanner in the works the following year. Where Iceland's quota was just 0.3%, the Faroes' was 4.8%, but now they wanted a lot more. One Scottish source says: "The Faroes said, 'Our outlying neighbour is catching four times what we are catching. Unless you offer us a much better deal we are going our own way.'"

The two countries demanded 15% each of a quota that divides roughly one-third to Norway, one-third to the UK and one-third to other EU countries, the Faroes, Iceland and Russia. This would mean the UK losing about 60,000 tonnes a year of its mackerel haul, worth the best part of £50m, most of it Scottish.

The Scots and other fishing nations upped the pressure in 2010 by banning Faroese and Icelandic boats from landing hauls at their ports. This only hit the Faroese, since the Icelanders have enough processing capacity at home, though it also hurt the Scottish and Norwegian processors that would have got much of the business.

Last August this led to two blockades at Peterhead, when Faroese ships were prevented from landing by angry fishermen. Negotiations dragged on without a deal and have now broken off until the 2013 negotiations start in the autumn. The best deal the two countries have been offered is 7% for Iceland and 8% for the Faroes, but they dismissed it out of hand. Last year they caught 146,000 tonnes and 150,000 tonnes respectively, compared to the UK's 192,000.

"The Faroes only have seven vessels," says Ian Gatt, chief executive of the Scottish Pelagic Fishermen's Association. "Offering them nearly double their quotas is like them winning the EuroMillions lottery.

"Iceland are going from zero catches in 2004 to being offered a substantial stock. It's pretty galling. We have 50% of the EU share so we would be hit hardest. We want to see them tabling a counter proposal but so far they haven't moved an inch."

According to Jogan Jerspersen of the Faroese Pellagic Organisation, the reason his country has not made a counter proposal is because the EU/Norwegian offer was "not enough to get us in a process". He says: "Almost the whole Faroese economy depends on fishing. When it's fish in our area, we must have a share of it."

He adds that banning Faroese landings in Scotland has led to a new processing factory on the islands and means Scottish processors will never get as much of the work from his members that would have come if they had done a deal earlier.

Fridrik Jon Arngrimsson, his counterpart in Iceland, says all countries are to blame for the failure to meet the quotas and that his fishermen would lower their quotas proportionately if others would do the same. "Fortunately, we feel the stock is in better shape than the scientists believe," he says. "Some EU countries used to fish much more than reported, so the species might be able to cope with more. However, you cannot count on that and so we need to keep to the recommendations."

This will be taken as a reference to the Scots, whose industry is in the process of being fined hefty amounts for conspiring to break quotas in the early 2000s.

Whatever the case about the science behind the quotas, though, fishermen expect that the loss of their sustainable fishing accreditation will be followed by tougher quotas. They might not fish for cod, but they know the North Atlantic was, until recently, full of that fish, too. Regardless of the rights and wrongs of the competing claims, many expect 2012 to be a high watermark for mackerel.

Whether by doing a deal with northern neighbours or holding out until the EU forces change, it is hard to see such good times ahead. Like white fishermen before them, the mackerel men are going to have to adjust to a new reality.