Governors and their deputies at the country's jails are receiving extra payments of up to £10,000 a year to stop them resigning.
Labour MSP Lewis Macdonald hit out at the income top-ups, while a leading trade union officer said there was "huge concern" about the system.
The Scottish Prison Service (SPS) manages 14 jails and is responsible for around 4000 staff.
In common with other parts of the public sector, the SPS workforce has undergone a redundancy round and endured static wages.
But the Sunday Herald has learned of a scheme that has managed to give prison bosses extra money.
Around 70 "recruitment and retention allowances" (RRA) are paid out every year to senior staff. Some managers can get a top-up of £2500 to £5000 a year, while their superiors can be entitled to the £10,000 maximum – a 15% salary boost.
A limited number of RRAs were doled out in the early part of the last decade as a way of holding on to certain types of staff.
But in 2009, SPS bosses decided to widen the scheme for prison governors. They did so on the grounds that an "unprecedented" number of senior employees were leaving for lucrative private-sector posts.
However, an internal SPS briefing posed a series of awkward questions about extending RRAs to governors and their number twos.
One of the questions was: "Doesn't it just feel wrong to be awarding this kind of allowance at this time?"
The same document asked another question: "Last year the SPS general pay increase was 2.35%. How can it be right to award Recruitment and Retention Allowances of many times that?"
It also stated that paying RRAs to senior managers could be "potentially divisive", adding: "Wouldn't it be better to leave things as they are?"
Despite the qualms, the SPS pushed ahead with the extension.
According to figures obtained by this newspaper, the 68 RRAs paid out in the last financial year cost the taxpayer £378,940.
In the last three years, the "golden handcuff" payments came to £1.1m.
Earlier this year, the Prison Officers Association in Scotland passed a motion condemning the RRAs for senior staff.
The motion called for a "Government led investigation into the legality and ethics of such an undertaking ..."
Scottish Labour's Lewis Macdonald MSP, said: "It simply isn't acceptable for top managers to receive bonuses for no other reason other than they haven't resigned.
"Our prisons continue to become ever more over-crowded, staff pay is frozen, prisoners aren't accessing suitable training or educational opportunities and yet senior managers receive substantial rewards. What's good enough for prison officers should be good enough for governors, too."
Albie O'Neill, industrial officer for the Public and Commercial Services Union, said: "To have senior staff receive £10,000 in added payments is a huge concern. These allowances were introduced behind closed doors. By contrast, most staff have received a pay cut in real terms. These RRAs could also be a breach of equal pay legislation."
An SPS spokesman said: "In recent years a number of senior staff have left SPS, to join either private sector companies or other jurisdictions. These allowances were introduced to retain the services of staff who are considered key to the successful running of our prisons."
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