Mogudishu authorities feared withdrawal of troops will create dangerous security gaps in the country.
Kagame is eligible for 10 more years in office under the constitution that will see him serve as president for 40 years if elected.
South Sudan has been facing another extension of transition period with doubts raised on the state’s ability to hold elections next year.
This surprise turn around comes just days after Atmis handed over Bio Cadale FOB in HirShabelle State on September 17.
Blinken expressed appreciation for Kenya’s long standing strategic partnership with the United States.