One gunman was among the dead while another was hospitalised along with two children who were inside the house, interior ministry spokesman Mohamed Ali Aroui told reporters at the scene.
He said one of the children, a girl, had suffered a head injury but did not elaborate on their conditions.
"Special forces approached the kitchen where the terrorists were hiding," Aroui said.
"The women came out of the kitchen firing," he added, describing both the men and women at the house as "terrorists".
The house in Oued Ellil, a suburb of Tunis, was surrounded earlier the same day following the arrest of two suspected militants in Kebili, 500 kilometres south of the capital.
The confrontation came as security was tightened in the lead-up to parliamentary elections on Sunday - the first since the nation's revolution three years ago.
Officials say they plan to deploy tens of thousands of soldiers and police for the election, warning that "terrorist" elements are seeking to disrupt the vote.
Islamists suppressed under former strongman Zine El Abidine Ben Ali have proliferated since his overthrow in the 2011 uprising.
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