Mobile phone banking was introduced in the northern Somaliland region in 2009 and has now spread across the country.
Al-Shabab and its allies control much of southern Somalia and one mobile phone company official said he had “no option but to obey” the order.
Despite years of conflict, Somalia’s telecommunications sector is thriving.
Mobile phones are a common sight in the capital, Mogadishu, and three companies currently offer mobile phone banking.
But the al-Qaeda linked group has given them three months to stop.