Universities, quangos and the BBC shelled out the cash despite the Confederation of British Industry's (CBI) defence of public-sector cuts and wage freezes for staff.
Green MSP Patrick Harvie questioned why the bodies had signed up to the CBI in the first place.
The CBI, which acts as the voice of big business, was criticised recently when it formally registered as a No campaigner in the independence referendum.
As a result, the CBI was legally able to spend up to £150,000 of its budget campaigning to keep Scotland in the Union.
The move backfired after it emerged that some of its fee-paying members were public-sector bodies under the control of the Scottish Government.
Around 20 such bodies either terminated or suspended their CBI membership.
The CBI admitted a mistake and deregistered as a campaigner with the Electoral Commission.
CBI Scotland director Iain McMillan also confirmed his retirement from the organisation during the row, although he said the decision had been made months ago.
The episode has also raised questions about why public-sector organisations had ever chosen to join.
According to newly released figures covering three years, 14 public bodies have topped up the CBI's coffers.
Scottish Enterprise paid around £42,000 in fees, while Highlands and Islands Enterprise coughed up over £15,000.
Tourism quango VisitScotland diverted nearly £32,000 to the CBI over three years, Skills Development Scotland paid over £66,000 and the Scottish Qualifications Authority gave around £40,000.
The BBC, whose CBI membership angered some staff, has paid £65,000 to the business group since 2011.
Scotland's university sector, which has presided over thousands of job losses, has also boosted the CBI's bank balance.
Heriot-Watt joined in 2013 at an annual subscription rate of £12,000, while Glasgow Caledonian doled out around £37,000 in three years and Robert Gordon University handed over around £24,000.
In the same period, Glasgow, Strathclyde, Edinburgh and Dundee universities respectively paid around £11,000, £29,000, £36,000 and £19,000. Aberdeen contributed another £34,000.
All told, the public-sector bodies paid around £460,000, but some of the figures excluded VAT.
Harvie said: "The deeply unprofessional way the CBI has handled itself during the referendum campaign has quite rightly led to an exodus of members. The confirmation that public bodies have given this anti-independence, pro-privatisation organisation half-a-million pounds will leave many taxpayers astounded.
"The big question for these public bodies is why they signed up to a lobby group that approves of austerity, wants to sell off Scottish Water, and generally advocates the kind of light-touch regulation that led us into economic wreckage."
Tory MSP Murdo Fraser said: "The CBI is a very well-respected and credible lobbying and networking organisation, and it's entirely understandable that a range of public-sector bodies would see value in membership.
"It's very disappointing that there are those in the Yes camp who have sought to make political capital out of this."
CBI Scotland was unavailable for comment when the Sunday Herald tried to contact it yesterday.