More than 60 wounded in attack on popular seaside spot frequented by Somalis on weekends.
President Hassan Sheikh Mohamud has called a meeting of regional leaders.
Rift comes after Somaliland deal giving landlocked Ethiopia access to the Red Sea.
Mogadishu also shuts down Addis Ababas consulates in Hargeisa, capital of the Somaliland, and Garowe in Puntland.
MV Abdullah was sailing from Mozambiques capital Maputo to the United Arab Emirates when it was attacked.
The armed group considers the United Arab Emirates an enemy for its backing of the Somali government.
Mogadishu says a deal to grant Addis Ababa access to sea in Somaliland is a violation of its sovereignty.
Despite a government offensive against the armed group, al-Shabab shows its capacity for high-level attacks.
Several passengers reportedly taken after helicopter lands in territory controlled by the armed group.
Ethiopias economy has struggled with no sea access, and an agreement to use a Somaliland port has upset its neighbour.