The self-declared republic located in north-western Somalia is protesting Sunday's move by Mogadishu to assume full control of Somali's entire airspace, including that of Somaliland.
It is the first time the Somalia is taking control of its airspace following two decades of anarchy triggered by the collapse of the central government in 1991.
On Tuesday, Mohamud Hashi Abdi, Somaliland's Civil Aviation minister, issued the ban against UN agencies alleging that UNDP and the Nairobi-based Civil Aviation Caretaker Authority of Somalia (CACAS) had violated a previous agreement between Somalia, UNDP and the Somaliland administration.
"We had already signed an agreement which allows an independent panel to control the airspace," Minister Hashi told the media at Hargeisa, Somaliland's capital, some 1,500km northwest of Mogadishu.
"Unfortunately CACAS and UNDP seem to be siding with [the] Mogadishu government."
The ministerial order states that effective May 15, no UN flights will be allowed to land at Somaliland airports.
On Sunday, Somalia indicated its intention to consolidate control over its airspace by relocating its civil aviation office from Nairobi.
"The federal government (of Somalia) will relocate more than 100 airspace management staff based in Nairobi to Mogadishu by end of this year," Somalia’s Information, Posts and Transport Minister Abdullahi Elmoge Hersi told reporters.
Mr Hersi added that the airspace control office, which will now be based at Mogadishu’s Aden Abdulle International Airport, would maintain close collaboration with Nairobi’s civil aviation authorities during the move.
No country has yet recognised Somaliland, which snubbed the recent high-profile conference on Somalia in London.