Most MoD civil servants no longer believe their managers can steer them through difficult times, feel more negative about almost every aspect of working for the MoD than they did a year ago, and their morale is much worse than the rest of the civil service.
The revelations have prompted a fierce reaction from trade unions and a former MoD official, who confirm that the workforce is deeply demoralised, upset and angry. According to one union, the words most often used to describe MoD management are "incompetent, short-sighted, inept, poor, uncaring and self-interested".
The leaked survey was conducted by the US opinion research company, ORC International, as part of an annual questionnaire of the entire civil service. It received responses from nearly 33,000 staff, 44% of the MoD's workforce.
Overall, only 22% felt positive about the MoD's leadership, three points less than in 2010, and 16 points below the median for the civil service. Just 9% agreed that "when changes are made ... they are usually for the better".
Only 17% had "confidence in the decisions made by MoD's senior managers", three points down on the previous year and 19 points below the civil service. One-fifth of the workforce wanted to leave the MoD as soon as possible or within the next 12 months, four points higher than in 2010.
"This is a clear vote of no confidence in the leadership of the MoD," said Steve Jary, national secretary of the trade union, Prospect, which represents 7000 MoD specialists.
"Staff morale is going from bad to worse," he added. "The level of concern and even anger is astonishing. These views are not borne out of self-interest. They betray a deep concern about the safety and effectiveness of our armed forces."
According to Prospect, 5500 staff are leaving the MoD this financial year, and another 7000 redundancies are being sought. "The continuing loyalty and commitment of staff is being brought into question by members' attitude to working for the MoD," Jary warned.
The MoD's overall aim is to cut 32,000 jobs, according to the Public and Commercial Services Union (PCS), which represents 18,000 MoD civil servants, 2000 of whom work in Scotland.
"No account has been taken of the effects this will have on existing staff," said Ian Fraser from PCS.
"No wonder staff are demoralised, fed up and do not believe a word the MoD says about being interested in their views."
The leaked survey showed that only 18% of staff believed MoD managers "will take action on the results from this survey", six points less than in 2010.
One recent example of why morale is so low occurred during the fierce storms on December 8. Although private-sector staff at the Faslane naval base on the Clyde were sent home early, some MoD civil servants were told to remain at their posts.
This made MoD staff "very angry", Fraser said. "We intend to challenge the MoD and ask why the safety of their staff was not as important as it was for the other employers at Faslane. Situations like this only demoralise further."
Fred Dawson, a former senior MoD safety official, warned that the cutbacks could put nuclear safety at risk because staff fear for their jobs.
"The continuing cuts are resulting in a serious lack of confidence in the decisions made by MoD's senior managers," he told the Sunday Herald. "Staff are far more likely to give managers the answers they want to hear rather than the truth. In safety-critical situations such as MoD's nuclear programmes, they may well be reluctant to raise safety concerns for fear of being marked out for redundancy."
The MoD pointed out that it was facing job reductions and major reform. "Although the results of the survey are disappointing, they are not surprising," said a MoD spokeswoman.
"The results confirm our need to improve working in the MoD and reduce uncertainty for our staff. We will continue to ensure we are delivering a more positive and inclusive approach for the future of defence."
During the recent storms risk assessments were carried out which concluded that there was no requirement to close Faslane, she added. "Any non-essential MoD staff were allowed to leave and return home if they wished."