All of the NCVO's 135 staff are going through a job-evaluation scheme that might lead to their salaries being increased or reduced.
The umbrella body has asked employees to complete forms outlining their responsibilities to help decide whether they are being paid appropriately.
A source at the NCVO, who did not want to be named, said some staff were worried about completing the exercise in case their salaries were cut.
A spokesman for the NCVO said the organisation came up with a new evaluation system after a review in 2007 indicated that staff and managers were unhappy with the old process.
"We haven't heard of any staff being disgruntled," he said. "Everyone is playing a positive and full role in the process and all staff are being consulted."
The review is expected to be completed by early April.