Scores of people took to the streets in Kismayo, south of the capital, Mogadishu, on Friday, burning tyres and blocking roads, after the Islamists appointed a new governor, mayor and heads of the airport, port and the city's overall security.
The protesters said the Islamists, who captured Somalia's third city on September 25, had not shared power fairly when picking the port's new leadership.
"We are angry about how this administration has been set up," said Barre Ahmed, an official of the Juba Valley Alliance, an independent authority that controlled the region around Kismayo before the Islamists took it over.
However, the Islamists said the protesters were political trouble-makers.
Abdul Kadir Jibril, one of the Islamist officials charged with security in Kismayo, said: "We have arrested 35 people. These were not regular demonstrators, they have a political agenda to undermine our administration."
The protests were the fourth since the Islamists seized the port.
Demonstrations have previously been held against the Islamists' ban on the leaf stimulant khat and on cinemas.
The Islamists, who control Mogadishu and large swaths of the south, seized Kismayo without firing a shot.
They now flank the country's weak interim government, based in the provincial town of Baidoa, on three sides.
The United Nations refugee agency said on Friday that more than 2,000 Somalis have fled across the border to Kenya in the past two days after reports of advances by Islamist forces on several southern towns this week.
About 30,000 people from Somalia have sought refuge in Kenya since the beginning of the year.
The interim government regards Kismayo's capture as breaching a ceasefire agreement reached at peace talks in Sudan.