Rassie Erasmus will leave Munster at the end of this year to become South Africa's director of rugby, while Jacques Nienaber is also on his way out of Thomond Park.
Erasmus only took over as Munster's director of rugby a year ago, but has agreed to return to his homeland at the end of December.
Defence coach Nienaber will depart at the same time as his compatriot Erasmus to take up a role as SA Rugby's high performance coach.
Jerry Flannery and Felix Jones will stay on as forwards coach and backline and attack coach respectively.
Munster will work with the Irish Rugby Football Union to identify potential replacements for the duo, who played such key roles in the province's run to the Pro12 final and the last four of the European Champions Cup.
"With the squad and management returning for pre-season this week we can today confirm that Rassie and Jacques will return to South Africa." Munster Rugby CEO Garrett Fitzgerald said.
"While we understand Erasmus' reason to return to his home country for an opportunity as the national director of rugby we are disappointed to see him and Jacques both leave. Working closely with both I witnessed first-hand the work that they do, and we will always be grateful to Rassie for leading the squad through our most difficult time with the untimely passing of [head coach] Axel [Anthony Foley].
"I believe we were very lucky in securing Rassie and Jacques in the first place, and we are thankful for the services of such experienced and knowledgeable coaching talent.
"Rassie succeeded in getting us back on track with much of the same personnel and when you see how far we have come and what we have gone through as a squad and organisation I am confident we will successfully manage the next stage. As a group we will be all the better for their input with Jerry and Felix now ready to step up to the next level.
"We have been in this position before, whereby our coach has been offered a national role and we are not going to stand in the way of someone in that regard. We understand Rassie's decision, and all parties are working together in managing the situation."