Protesters blocked the main street in the coastal town of Zarzis, shouting "the people want our lost children!"
The incident came more than two weeks after a boat carrying Tunisian migrants went missing off the coast during an attempt to reach Italy.
On Monday, seamen found eight bodies which are now awaiting DNA analysis to determine whether they are of missing Tunisians, the Tunisian Red Crescent said.
Families of the missing have been calling on authorities to step up search efforts.
They have also been angered by reports that three Tunisians were buried in the cemetery for foreign migrants, mostly from sub-Saharan Africa, whose bodies regularly wash up along the coast after tragedies at sea.
"The authorities wouldn't let sailors go out looking for the missing," said rights activist Mabrouka Dhaoui. "They buried out sons in a cemetery for foreigners, they should be ashamed of themselves."
Said Ben Zaid, governor of the surrounding Medenine province, told local radio that four bodies had been exhumed from the migrant cemetery to undergo DNA analysis.
The Tunisian Human Rights League said authorities had "not devoted the necessary resources to search and rescue operations in a timely way" and called for an inquiry into the burials.
The North African country has a long Mediterranean coast, in places just 130 kilometers (80 miles) from the Italian island of Lampedusa.
A long-running economic crisis has pushed many Tunisians to attempt the journey.
Despite generally favorable weather from spring to autumn, the journeys on barely seaworthy boats often end in tragedy.
Tunisian authorities intercepted nearly 200 migrants attempting to reach Europe northwards across the Mediterranean Sea over the weekend, the defense ministry said Tuesday.
According to official figures, more than 22,500 migrants have been intercepted off the Tunisian coast since the start of the year, around half of them from sub-Saharan Africa.