Rory Cullinan, head of the new mini "bad" bank inside RBS, was on Tuesday awarded £533,000 of shares, the equivalent of 100% of his salary so far this year.
The fresh "fixed share allowance" payment comes just two months after Cullinan collected more than £600,000 worth of shares in the first instalment of his £2.5m 2013 bonus.
RBS, which is 81% owned by the government after its £45bn bailout during the 2008 financial crisis, lost £8.2bn last year – its sixth year of consecutive losses that have also totalled £45bn since its rescue by taxpayers.
The bank wanted to pay its executives the equivalent of 200% of salary but was blocked by the Treasury in April.
It means RBS is limited to paying out up to 100% of salary – the maximum allowed by new EU rules without the express permission of shareholders. RBS is the only big UK bank that is being prevented from paying 200% bonuses. The government supported 200% bonuses at Lloyds, which was also bailed out by taxpayers and is now 25% owned by the state following the sale of shares to the private sector.
The Treasury told RBS that "there will be no rise" while the bank is "still in recovery". The chancellor, George Osborne, said: "We made it clear that in the circumstances it was not right to increase the bonus cap.
"We're moving from a situation a few years ago where bonuses were out of control, banks were being bailed out, [and] our economy was shrinking, to the situation we've got now, where bonuses are down, banks are recovering, and our economy is growing."
RBS has warned it faces an "exodus of talented staff" if it is unable to match the pay levels offered by rivals. Penny Hughes, the non-executive director who chairs the remuneration committee, said: "I know it is not always easy to accept, but if RBS is to thrive we must do what it takes to attract and keep the people who will help us achieve our goals.
"While we are sensitive to public opinion, particularly given our ownership structure, the ability to pay competitively is fundamental to getting RBS to where we need it to be."
The new shares, which are awarded for the eight months to the end of August, can be cashed in 20% chunks each year for the next five years. Fresh awards will be made every six months, and are not subject to Bank of England rules on clawbacks that were designed to retrospectively recoup bonuses in the event of any wrongdoing emerging in the future.
Chris Sullivan, RBS's deputy chief executive, was awarded £467,000 worth of shares. Sullivan hit the headlines last month when Andrew Tyrie, chair of the Treasury select committee, accused him of being "wilfully obtuse" in evidence to parliament.
Sullivan had told the committee that RBS's controversial global restructuring group (GRG) was "absolutely not a profit centre" but was later forced to write to Tyrie admitting, that on an accounting basis, the operation was run as a profit centre.
RBS last week announced it was closing down the GRG division, which is being investigated over allegations that it profited from the financial distress of small companies it was meant to help.
GRG has been the focus of allegations – notably by Lawrence Tomlinson, an adviser to the business secretary, Vince Cable – that it forces viable small businesses to the brink so the bank can buy up their properties and make a profit.
Ross McEwan, RBS chief executive, did not receive a share award after foregoing bonuses. However, in June he received shares worth almost £1.5m as part of a £3m signing-on deal. His basic pay and benefits stretch to £1.3m.
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