The poll found less than one-third of workers would recommend the Crown Office and Procurator Fiscal Service (COPFS) as a good place to work and only one in five said they could speak out about problems without fear of reprisals.
Of the 1032 staff surveyed, 165, or 16%, said they had been bullied, up from 142 last year, while one in seven claimed to have suffered discrimination by managers or colleagues.
A further 114 staff wanted to quit as soon as possible, with 93 keen to leave within the next year.
Only 30% said they would recommend COPFS as a good place to work, down by 3% on last year and 17% lower than the civil service average, while 97 said they had been bullied by a boss in the past 12 months.
Fiona Eadie of the First Division Association, the union for senior civil servants, said: "These survey results confirm the concerns we are hearing from members about falling morale and increasing workloads. Worryingly, even among our senior most senior members, only just over half think effective action has been taken since the last survey."
COPFS chief executive Catherine Dyer said: "We do not tolerate any form of bullying, harassment or discrimination. Any instances reported are investigated thoroughly."