The group admitted illegally landing mackerel and herring worth £47.5 million between January 2002 and March 2005.
Fisheries Secretary Richard Lochhead welcomed the fines, saying they showed how seriously Scotland takes breaches of fishing quota laws.
The "black fish" scam was carried out at fish processing factory Shetland Catch in Lerwick, Shetland.
Judge Lord Turnbull called the case "an episode of shame" for the fishing industry, and said it was a "cynical and sophisticated" operation.
Hamish Slater, 53, and Alexander Masson, 66, both from Fraserburgh, were fined £80,000 and £50,000 respectively. Alexander Wiseman, 60, from Banff, was also fined £50,000.
Fines were imposed on 13 men from Shetland for their role in the scam.
Robert Polson, 48, was fined £70,000; John Irvine, 68, was fined £80,000; William Williamson, 65, was fined £45,000; Laurence Irvine, 66, was fined £80,000; and David Hutchison, 66, was fined £40,000, as was 56-year-old Thomas Eunson.
Both Allister Irvine, 63, and Gary Williamson, 52, were fined £35,000, and George Henry, 60, was fined £12,000.
John Stewart, 57, was ordered to pay £15,000, while George Anderson, 56, must pay £12,000.
Colin Leask, 39, and Allen Anderson, 55, were each fined £3000
A £70,000 fine was imposed on Victor Buchini, 51, from Poulton-le-Fylde in Lancashire.
The company Alexander Buchan was fined £240,000 for helping the vessel masters land the undeclared fish.
The pelagic fishermen, who committed the offences to evade the annual EU fishing quota, had already been ordered to hand over almost £3m under confiscation orders at a previous court hearing.
The convictions came as the result of a seven-year investigation, Operation Trawler, after the Scottish Fisheries Protection Agency (SFPA), now Marine Scotland, became suspicious about widespread illegal landing of fish within the pelagic fleet. Pelagic fish are those which swim near the water's surface.
Lord Turnbull said the proceedings brought "embarrassment and shame" to the skippers and their families.
He said: "All of the accused who appear today have spent their working lives as productive and hard-working members of our community. Barring other regulatory infringements, not a single one has ever come into any conflict with the law.
"It was not surprising therefore to hear of the well-respected positions within their communities which many held and of the embarrassment and shame which these proceedings have brought to them personally and to their families."
The judge noted that each master involved "made no attempt" to disguise his true income from the fish and paid income tax on both the declared and undeclared landings.
But he said the men had all participated in "a deliberate and calculated determination to evade the quota levels for fishing available to each vessel" for "purely financial" reasons.
He said: "The system through which this was achieved was both cynical and sophisticated and involved the connivance of a number of different interested parties, some of whom have benefited but have not been prosecuted.
"The extent to which landings of fish were deliberately under-declared was at times truly staggering and in the case of some of the accused concerned, took place continuously over a three-year period."
Responding to the news, Dr Mireille Thom, senior marine policy officer for environmental campaigners WWF Scotland said: "Landing 'black fish' isn't a victimless offence. Such landings not only undermine the conservation of fish stocks and the fortune of the fleets that fish them, they also distort competition by depressing fish prices."
Mr Lochhead said: "These cases demonstrate Scotland's commitment to transparent, sustainable fishing in our waters backed up with effective enforcement. It is important that all countries in Europe do what we have done in Scotland by stamping out such illegal activity."