Somalia's Foreign Affairs Ministry on Tuesday announced that the country had declared South African Nicholas Haysom the UN Chief in Somalia persona non grata.
In a letter Foreign Ministry said Somalia's Ministry of the UN envoy was "not welcome and cannot operate" in the country.
The Ministry accused him of "violating protocols" and "deliberately interfering" in Somalia affairs.
The move follows a letter issued on December 31 where Haysom asked about the government's legal basis for arresting Mukhtar Robow.
The letter questioned the Baidoa shooting of civilians in the protests that followed Robow arrest.
Haysom asked the government what action has been taken to investigate circumstances surrounding the deaths of civilians in Baidoa during the demonstrations.
The South African diplomat replaced Michael Keating in September 2018.