Wealthy health service managers will now be able to pocket salary increases of 4%, which could boost annual pay packets by over £6000.
By contrast, it was revealed yesterday that a 1% rise for NHS staff in England had been scrapped.
Finance Secretary John Swinney has largely followed the UK Government's policy of freezing the salaries of top and middle-income earners, while sanctioning limited rises for the low paid.
Until last month, this policy also applied to employees in the higher echelons of the health service.
In 2012-13, the SNP Government enforced a pay freeze for all NHS executives and senior managers, which covered those earning between £43,060 and £173,840.
However, the freeze was offset by a 1% "performance" related top-up for senior staff earning up to £77,276.
The new policy for 2014 is far more generous and is not restricted to middle-income earners.
All senior managers and executives, including those earning around £170,000, will be eligible for a rise of up to 4% if their performance is good enough.
A manager on £100,000 could be in line for a £4000 salary boost, while an NHS director could get up to over £6000.
It is understood the U-turn was made after NHS executives expressed unhappiness at their frozen pay.
At a conference last month, Neil hinted at a rethink when he said he was aware of "the concerns that now exist following several years of pay restraint".
He said of the new policy: "This settlement will be better than in recent years, but I accept that questions will remain about whether the management pay arrangements introduced by the previous administration continue to be fit for purpose."
Jon Restell, chief executive officer of Managers in Partnership, the trade union for senior NHS staff, also said at the time: "The current pay system for senior managers in NHS Scotland is not up to the job and it could be challenged by people under equal pay legislation."
Neil Findlay, Scottish Labour's health spokesman, said: "Staff and patients on low pay will find it unbelievable that senior managers already on hefty salaries could get a 4% performance-related pay award when complaints about the NHS are up, bed numbers are down, targets are being missed, IT systems failing and patients are being treated in cupboards."
Liberal Democrat MSP Jim Hume said: "The potential to give already well-paid managers in the NHS a generous pay increase of up to 4%, and in some cases 5%, seems hard to justify especially when the pay increase for nurses is capped. This will do little for the morale of frontline staff and does nothing to encourage new people into the NHS."
A Scottish Government spokesman said: "Unlike other NHS staff groups, senior managers have had their pay completely frozen in recent years, including for pay progression. This settlement will continue to be in line with pay policy.
"It is important to note that automatic increments for doctors, nurses and other clinical staff are 3.5% to 4%, hence total increase for any manager will not exceed that."