John Woodhatch, 58, from Epping, Essex, was sentenced to five years in prison and Adrian Taylor, 44, from Swanley, Kent, was handed a six year sentence after both pleading guilty to charges of money laundering.
The scam involved a payment diversion fraud linked to the construction of a new runway at the airport on the island.
An investigation by the City of London Police led to the duos convictions.
Woodhatch and Taylor contacted the Guernsey Treasury in June 2012 claiming to be from Lagan Construction, which is currently carrying out a £50m project at the airport.
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The pair informed officials they wanted to change the bank account details into which the Treasury was making its monthly payments to the company.
Once the latest payment of £2.6m had been transferred to a RBS account Woodhatch, who was working as a city broker, immediately instructed the bank to move the funds to accounts in Dubai and Turkey.
Woodhatch told RBS that the transfers were mainly to pay for a horse in Dubai.
However, the banks money laundering team referred the matter to the City of London Police for investigation in July 2012.
Within days detectives, assisted by Guernsey Police, had arrested Woodhatch and searched his home and commercial addresses.
A review of the accounts found that £52,000 of the stolen funds had been transferred to Adrian Taylor. He was arrested in October 2012 after handing himself in to police.
Det Insp Rob Stirling, who led the investigation, said the scam should serve as a warning to other public and private sector bodies that could be targeted by fraudsters in the same way.
(LM/MH)
