The order comes days after the official, Nicholas Haysom, raised concerns at the action of Somalia's UN-backed security services in recent violence that left several people dead.
"The Special Representative of the UN Secretary-General for Somalia, Nicholas Haysom, is no longer welcome in Somalia and cannot operate in the country," the foreign ministry said in a statement late Tuesday.
There was no immediate reaction from the UN mission in Somalia.
Somalia's security forces used force to put down three days of demonstrations in the southwestern town of Baidoa on December 13-15, with at least 15 people killed and 300 people arrested, according to the UN.
Protesters were angry at the arrest of Muktar Robow, a former Islamist leader who was vying for the post of regional presidency of South West State.
Robow, who defected from the jihadist Al-Shabaab movement in 2017, was detained by the government accused of seeking to "undermine stability", and flown to the capital Mogadishu.