The performance-related pay system was introduced in October last year and was opposed by 95 per cent of staff, according to a Unison survey last November.
Union bosses are planning a meeting with Scottish Enterprise chief executive Jack Perry. A Careers Scotland spokeswoman said: "We are disappointed Unison feels the need to do this. We have offered the unions the chance to take part in discussions and our door remains open."
She added: "We are aware that there are some concerns about performance-related pay and we are working with colleagues to introduce the process as smoothly as possible."
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