The scam allowed the fishermen to land more mackerel and herring than they were allowed under EU quotas.
Scales at Lerwick-based processing company Shetland Catch Ltd were set to underestimate the weight of the fish being landed by the boats.
Seventeen skippers have previously admitted their part in the scam.
Earlier this month they were ordered to hand over almost £3m in confiscation orders.
They are due to be sentenced next month.
The BBC had challenged the reporting restrictions which had prevented the reporting of the extent of the false declarations to the Scottish Fisheries Protection Agency, and the method used to make the undeclared landings.
Weighing scales at Shetland Fisheries were linked to computer screens showing the weight of fish landed.
The screen in the main floor of the fisheries, which was viewed by SFPA officials, was set to give a lower weight of fish than had been landed.
The proper weight was displayed on a screen in the engineer's room, in a part of the operation which was off limits to SFPA officials.
The SFPA had launched an investigation due to suspicions of widespread illegal landing of pelagic fish.
Accountants found that Shetland Catch Ltd's outgoings could not be supported by declared earnings.
The company has been taken over since its involvement in the scam, which took place between February 2003 and March 2005.
The 17 skippers have been ordered to pay back sums ranging from £2,700 to £425,900. The confiscation orders are:
Laurence Irvine, 66, of Aviemore, Symbister, Whalsay - £210,700; Gary Williamson, 52, of Norvag, Symbister, Whalsay - £118,500; William Williamson, 64, of Westerlea, Symbister, Whalsay - £213,200; George Henry, 60, of Noonsbrough, Clousta, Bixta - £51,300; John Stewart, 56, of 57 King Harald Street, Lerwick - £41,300, and Colin Leask, 38, of Vaarhjem; Simbister, Whalsay - £12,000.
David Hutchison, 66 of Ankerhus, Hillhead, Symbister - £140,900 Robert Polson, 48, of 17 Breiwick Road, Lerwick - £371,300; Thomas Eunson, 56, of Westwinds, Symbister - £140,500; Allen Anderson, 55, of Solvei, Symbister - £2,700; John Irvine, 68, of Braeside, Symbister - £236,000 and Allister Irvine, 63, of Karinya, Symbister - £120,600.
Victor Buschini, 51, of Cuckoos Nest, Kiln Lane, Hambleton, Poulton Le Flyde, Lancashire - £341,000, and Hamish Slater, 52, of 8 Strichan Road, Fraserburgh - £425,900.
George Anderson, 55, of Harbourview, Symbister - £40,700; Alexander Masson, 65, of 89 Strichen Road, Fraserburgh - £283,000 and Alexander Wiseman, 60, of 3 Sandyhills Gardens, Banff - £196,000.