Kenya's Ambassador to Somalia Lucas Tumbo was on Thursday summoned by Somalia's Ministry of Foreign Affairs and handed a protest note.
The move came after an alleged violation of a Kenyan plane on Somali airspace on Saturday when it landed at Kismayo Airport without any official permission.
Somali's Minister Abdulkadir Ahmed-their Abdi, who handed him the protest letter, said Somalia strongly protests the violation and will not accept any encroachment on its air, sea and land borders.
He said Kenya must respond to the breach because its troops stationed in the Lower Juba region are part of the African Union Mission in Somalia (Amisom).
"The Federal Government of Somalia sees this action contradicts all principles of good neighborliness and non-interference in the internal affairs of states," the minister said.
But sources at Kenya's Ministry of Foreign Affairs said the letter is in bad faith because the plane was not Kenyan.
"That was a private jet, and even if you look at those on board, they were of Somali origin, so how it turns out to be a Kenyan affair is not clear," the source said.
The source said the jet was cleared from JKIA and destined at Kismayo.
In July this year, Ambassador Tumbo was also summoned over what Somalia termed an offensive tweet by Principal Secretary Macharia Kamau.
Somalia then said it considered the tweet "an affront to Somalia's sovereignty, unity, and territorial integrity as well as harmful to the relationship between Somalia and Kenya".
Last month, Somalia ordered all aircraft originating from Kenya to land in Mogadishu.
The directive indicated that Mogadishu would vet all goods and people entering the country.
"International and local flights from and to Kismayu must route via Mogadishu," the government's aviation bulletin said.
Previously, the aircraft were allowed to land in Kismayu, Mogadishu and Garbaharey airports on top of tens of airstrips across the country.
"They are technically punishing the traders who travel to Kismayu, the economic hub of Somalia. Since, if you live Nairobi you have to go through Mogadishu to access Kismayu. From Kismayu, you will have to travel to Mogadishu, Wajir and then back to Nairobi," a Somali businessman told the Star.