Sir George Mathewson, former chairman of the Royal Bank of Scotland and the current chairman of the Scottish Economic Council, told the BBC Scotland news website this was the "direst and worst day for a long time".
"I obviously welcome the stability introduced to the banking system but it is deeply regrettable that we have, effectively, government ownership of a large part of the banking system," he said.
"I am confident the banks will pick up eventually but we are looking at a dire economic situation just now."
BBC business editor Robert Peston said the move would change the way banks operated.
"Taxpayers would end up owning about 60% of Royal Bank of Scotland and about 40% of a super retail bank formed by Lloyds TSB buying HBOS," he said.
"That's what has been announced by the Treasury, in what will count as perhaps the most extraordinary day in British banking history."
Chancellor Alistair Darling told BBC Radio Scotland that Sir Fred Goodwin and Sir Tom McKillop had waived their contractual entitlements.
"I think they have decided to do the right thing there," he said.
He said RBS, Lloyds TSB and HBOS would be run "at arm's length" from the government, and ministers would not be involved in day-to-day decisions.
Sir Tom McKillop said: "It is immensely regretful that we are coming to shareholders to raise funds again.
"This is something that we certainly feel bad about."
The government is to appoint three directors to the RBS board and two to Lloyds TSB.
The new chief executive of RBS will be Stephen Hester, who is currently the chief executive of British Land.
He joined the RBS board as a non-executive director during the summer in a move widely seen as a precursor to Sir Fred Goodwin's departure.
Sir Fred Goodwin was nicknamed "Fred the Shred" for transforming banks through aggressive deals which resulted in staff losses.
His position had been under scrutiny after heavy losses as a result of the credit crunch, and since the £12bn rights issue earlier this year following the RBS takeover of ABN Amro.
Sir Fred Goodwin said the bank was "entering a new chapter that needed new leadership".
He insisted the takeover of ABN Amro had not caused the situation, and that there would have been huge write-downs with or without the ABN deal having gone ahead.
Sir Fred Goodwin, 50, attended a grammar school in Paisley before studying law at Glasgow University, working as an accountant with Touche Ross, Clydesdale Bank and Yorkshire Bank. He was knighted for services to banking in 2004.
Sir Tom McKillop meanwhile has spent most of his career in pharmaceuticals, latterly as chief executive of AstraZeneca. He joined Zeneca as a chemistry research assistant in 1969 when it was the drugs arm of ICI and rose to become chief executive after the merger with Astra, of Sweden.
He became one of the most highly placed RBS non-executive directors and combined chairmanship of the bank with a board seat at BP.
Oxford graduate Andy Hornby topped his MBA class at Harvard Business School and became chief executive of HBOS in 2006 aged 39.
He began his career at Blue Circle, the cement company, before moving to Asda, where he worked alongside Allan Leighton, chairman of Royal Mail, and Justin King, chief executive of J Sainsbury.
He also launched George, Asda's successful clothing brand, before moving to Halifax, which later merged with Bank of Scotland.
Dennis Stevenson, now Lord Stevenson of Coddenham, has been described as the ultimate eminence grise of British business.
He was chairman of consultants SRU before becoming chairman of Halifax, later HBOS, and of Pearson Group. He is also a director of The Economist.
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