"Having carefully assessed recent developments and exercising its constitutional authority, the Council of Ministers has annulled all agreements concluded with the United Arab Emirates... including bilateral security and defense cooperation agreements," the Somali government said in a statement.
There have been deepening differences between Somalia and the UAE over a number of issues.
The UAE is seen as quietly supporting the move by Israel last month to recognise Somaliland, the first to do so since the self-proclaimed republic declared independence from Somalia in 1991.
The UAE built and operates a large deep-water port and military base at Berbera in Somaliland.
Tensions spiked again last week after Saudi Arabia accused the UAE of helping a Yemeni separatist leader, Aidarous Al-Zubaidi, escape by boat and plane via Berbera and the Somali capital Mogadishu to Abu Dhabi.
Somalia's immigration agency said at the time it was investigating an "alleged unauthorised use of Somalia's national airspace and airports".
The Somali government did not directly mention the recognition of Somaliland or the alleged escape of Zubaidi in its statement cancelling deals with the UAE.
It said the decision was "based on credible reports and compelling evidence concerning hostile actions undermining national sovereignty, territorial unity, and the political independence of the country".
"The decision of the cabinet today comes after a long period of endurance by the leadership of the federal government. The UAE continued to interfere with Somalia's internal affairs and has been engaging in acts of misconduct and dual-track policy in Somalia," a senior official in the Somali presidential palace told AFP, on condition of anonymity and without going into details.
- Stoked fears -
Much of the international community, especially in the African and Arab world, opposed Israel's recognition of Somaliland, with many fearing it would stoke other seccessionist movements.
But the UAE has remained quiet.
Somaliland enjoys a strategic position on the Gulf of Aden and has its own currency, passport and army. It is seen as a useful launchpad for Israel to target Houthi rebels in Yemen or for the UAE to supply allies in Africa.
Somali President Hassan Sheikh Mohamud called the Israeli decision a "threat" to stability in the already volatile Horn of Africa.
In its statement on Monday, the Somali government said the UAE would no longer be permitted to operate in Berbera, although it has only theoretical authority over the region.
It said partnerships with the UAE at two other ports in Somalia -- at Bosaso and Kismayo -- were also cancelled, although these also lie in areas where the federal government has only limited control, in the semi-autonomous states of Puntland and Jubaland, respectively.
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