The officials were part of a government delegation scheduled to attend the launch of an European Union-sponsored cross-border conflict management programme on Tuesday.
Those denied entry are junior Minister of Water and Energy Osman Libah and legislators Ilyas Ali Hassan and Zamzam Dahir.
The three were, however, holding diplomatic passports.
According to the Somali officials, Immigration officials at JKIA told them that they should have obtained visas at the Kenyan embassy in Mogadishu before proceeding.
