The shells struck the southern Mogadishu suburb of Danwadagta near a security checkpoint for the airport in the Somali capital.
"Three civilians died and three others were wounded after mortar shells hit their house," said security official Abdi Muhidin.
"Two of the dead were a mother and her daughter and all of the victims belong to the same family," said witness Awale Yasin.
The attack is the second this week in Mogadishu after a car bomb at a restaurant left seven dead on Wednesday.
While the Al-Qaeda-linked Shabaab have lost large swathes of territory and were forced out of Mogadishu by African Union troops in 2011, they continue to strike in the capital and countryside.
Shabaab has not claimed any of the attacks, although they regularly carry out similar bombings and mortar strikes.
Somalia's President Mohamed Abdullahi Mohamed yesterday pledged a new war against the Al-Qaeda-linked Shabaab, giving militants 60 days to surrender or "face the consequences".
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