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Al-Shabaab claimed responsibility for the attack through a statement posted on its affiliated websites, claiming it killed 10 Kenyan soldiers and wounded several others.
Kenya wants Somalia to withdraw the maritime boundary case from the ICJ and end the row outside the court.
The relations between the two countries have been at the lowest point for the past eight months after Farmajo cut off ties with Kenya in December 2020.
He said the shelling followed a ground operation by Kenyan forces after Al-Shabaab attacked Jubaland forces traveling near Kudhaa in the Lower Jubba region early on Wednesday morning, which the militant group said killed 8 soldiers.
Somalia has submitted a complaint against Kenya to the UN, just two days after relations between the two countries return to normal.
The main AMISOM bases have been put on high alert as the group intensified attacks in Somalia.
A KDF convoy came under IED blast while passing through Baure village in Lamu County, prompting heavy fighting between Kenyan forces and Al-Shabaab fighters.