Relationship between Kenya and Somalia on Thursday took yet another nose dive with the controversial landing of Kenya aircraft at Kismayo Airport being the at center stage.

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The federal government summoned Kenyan ambassador to Somalia Lieutenant General Lucas Tumbo on Thursday where he was put to task to explain the circumstances.

In a statement to the media, Mogadishu warned that it would not tolerate any actions that leads to encroachment of Somali's sea, air and land.

"Somalia strongly violates this violation and will not accept any encroachment on its air, sea and through land. It's calls Kenya to respond to the breach because it's troops are stationed in Lower Juba region," read the statement.

"The federal government of Somalia sees this contradicts all principles of good neighbourhood and non interference of the state affairs,"

The aircraft in question, a Fokker 50 registered in Kenya as 5Y-JXJ, flew out of Nairobi on Saturday and arrived in Kismayu directly without stopping in Mogadishu first. It is operated by Jubba Airways, a Somali airliner that routinely flies to several Somali cities.

Aboard the plane were former federal state leaders Sharif Hassan Aden (South West) and Abdikarim Hussein Guled (Galmudug). 

There were also several Somali MPs heading to Kismayu ahead of the planned, but controversial, swearing-in of Jubbaland President Sheikh Ahmed Mohamed Madobe.

President Mohammed Farmaajo's administration had imposed flight ban on aircrafts landing in Kismayo, a move seen as a wider plot to thwart planned inauguration of President Sheikh Ahmed Madobe of Jubaland state.

A senior goverment official in Nairobi had accused Somalia of blackmail, insisting that the aircraft does not belong to any Kenyan government agency thus the complaints were null and void.

“It sounds like a smear campaign to portray Kenya as bad. But we aren’t bad, we are a law-abiding state. In fact, the responsibility to police aircraft movement in Somali airspace rests with the Somali government,” said a senior official discussing the matter on background.

Somalia has been at loggerheads with Madobe, who the federal government accuses Kenya of imposing him to the people of Jubaland. He's a close ally of KDF.

The flight, whose complaints have been registered at International Civil Aviations Authority, is said to have been under KDF's surveillance as it sneaked Somali leaders to Kismayo.

And a senior government official, who spoke in confidence, said KDF played a major role in organising for landing of an aircraft from Kenya to Kismayo Airport on Saturday.

"The KDF' team organised for the plane to carry senior Somalia government officials directly to Kismayo. Despite the fact that direct flights were banned, KDF was protecting the plane.

"There is nothing that could have happened. Kenyan government was keen to ensure the inauguration gets the status it deserves. KDF organised for transportation of the officials," he said without giving much details.

Already, Kenya is at loggerheads with Somalia over Indian Ocean maritime border, with the case now being handled by the International Court of Justice at The Hague.