Personnel from Somali Intelligence and security agency NISA have taken over Imam Khomeini centre in Mogadishu on Thursday evening.
The move follows after the government ordered complete halt to the operation of the Imam Khomeini humanitarian organization in the country and closure of Islamic republic embassy in Mogadishu.
Foreign ministry has also given Iranian diplomats 72 hours to leave the country.
Sources have also confirmed to Radio Dalsan that anti Iran and Shia slogans have been painted or sprayed at the Islamic republic of Iran embassy building in Mogadishu.
Somalia is among several Arab league states that have severed ties with Iran following arson attack on the Kingdom of Saudi Arabia embassy in Tehran earlier this week.
Neighboring Somali inhibited Djibouti also cut ties with Iran while ordering diplomats out on Wednesday.
The diplomatic relations between Saudi Arabia and Iran is at lowest since 1980s.