By introducing the well-being hour - a progressive and pragmatic initiative - the Welsh government hopes to be able to work with staff to address issues such as stress and mental health.
The deal was struck, in partnership with the PCS and FDA, as part of pay negotiations.
It will be built into normal working hours and chimes with other policies being implemented across the country by the government.
These include the Well-Being of Future Generations Act, a law seeking to improve the quality of life of people in Wales now and in the future, and the Welsh Prosperity for All Strategy.
Commitments in the strategy include: improving the health and well-being of workers with a specific focus in mental health and musculoskeletal conditions and delivering an in work scheme with rapid access to early work-focussed interventions on a range of conditions.
Prospect Welsh government branch secretary Robin Bradfield said: “The well-being hour is an excellent opportunity for the Welsh government to take a lead and further demonstrate its commitment to the physical and mental health and well-being of our members and staff generally.”
Welsh government permanent secretary Shan Morgan said: “Personal resilience and wellbeing is something I take very seriously – for myself and for the organisation as a whole. In common with many other organisations we have an aging workforce and sickness absence levels that have been difficult to shift in recent years.
“Last year, the board agreed a new well-being strategy designed to help us become a healthier workplace that supports colleagues to look after their physical and mental wellbeing. I see our new well-being hour as an innovative way of putting strategy into practice in a very practical way that I hope everyone will benefit from.”