Kenya has rejected a top United Nations (UN) court ruling that decided mostly in favour of Somalia in a maritime row, saying it was profoundly concerned by the boundary it set in a part of the Indian Ocean believed to be rich in oil and gas.

The International Court of Justice said in its ruling on Tuesday that the revised maritime border along the exclusive economic zones for the continental shelves of Somalia and Kenya had achieved an equitable solution.

"While Kenya is not surprised at the decision, it is profoundly concerned by the import of the decision and its implications for the Horn of Africa region, and international law generally," President Uhuru Kenyatta said late on Tuesday.

"At the outset, Kenya wishes to indicate that it rejects in totality and does not recognise the findings in the decision," he added in a statement.

He said the decision would "potentially aggravate the peace and security situation in the fragile Horn of Africa Region".

Somalia, which welcomed the ruling, filed the case in 2014 at the United Nations' highest court dealing with disputes between states.

Tuesday's ruling came after Nairobi last week said it had revoked recognition of the court's compulsory jurisdiction.

Kenya secured some territory beyond the Somali claim, but the court said it had failed to prove there was an established sea boundary between the states, which would have given it a greater portion of the disputed territory.

While Kenyatta described the ruling as a zero-sum game that would strain relations between Kenya and Somalia, he said Kenya aimed to resolve the dispute diplomatically.

"Kenya, as a key proponent of respect for the principle of subsidiarity ... will resolve this matter through the institutions of the African Union ... in addition to other bilateral arrangements," he said, adding he would do everything in his power to preserve its territory.

Admiral Abdi Hamiid Mohamed Ahmed, commander of Somalia's marine forces, said they were ready to guard their territorial waters.

"It was and is our sea, but other people desired to take it. There is no compromise. I will not talk about how many marine forces and equipment we have, but our forces are enough to protect Somalia’s waters," he told reporters in Mogadishu.