Foreign Minister Yusuf Garad Omar, Trade Mminister Khadra Ahmed Duale and Interior Minister Abdi Farah Said all lost their jobs.
No reason was given for the reshuffle, but it came amid criticism the government had failed to consult clan elders on their decisions.
They were replaced with men from their respective clans, on which much of Somalia's political loyalties are based.
Ahmed Ise Awad was named as new foreign minister, Abdi Mohamed Sabriye as the interior minster and Mohamed Abdi Hayr as trade minister.
The Shabaab has been fighting to overthrow successive internationally backed governments since 2007, and frequently deploys car and truck bombs.
In October, both the defence minister and army chief resigned and were replaced.
The police and intelligence chiefs, sacked in October after the country's deadliest attack killed 512 people, have yet to be replaced.
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