Some staff will receive a higher consolidated award due to progression payments, while staff on the maximum will receive an additional 1%, non-consolidated payment.
Members in PCS and FDA also accepted the offer and we hope the increases will be in July pay packets (with backdated pay to April also included).
Prospect negotiator Richard Hardy said: "We've expressed on numerous occasions our disappointment about the failure to make a real start on pay restoration for staff employed at Scottish Government but we recognise that there are constraints on what the Scottish Government can afford.
"However this pay rise at least ensures that members do not fall further behind in real wage terms and represents another substantial improvement over what our members employed by Westminster will receive. This is another indication of the influence of unions in Scotland."