Scores of people took to the streets, burning tyres and throwing stones early on Saturday morning, 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 the city, Somalia's third largest, on September 25, had not shared power fairly among various clans 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.
The heavily-armed Islamists fired shots to the air to break up the protest and then moved in to arrest the demonstrators.
Islamists: Protests illegal
The Islamists said the protests were illegal because they were organised by the group's politial opponents.
"These were not regular demonstrators, they have a political agenda to undermine our administration," said Abdul Kadir Jibril, one of the Islamist Court officials charged with security in Kismayo.
The Islamists newly appointed top security man Abdullahi Warsame said about 100 people had been arrested but promised to free those found to be innocent.
"We will not allow anyone to disturb peace," he said.
The protests were the fourth since the Islamists seized the port. Past demonstrations have also been against the Islamists' ban on qat, a popular leafy stimulant, and cinemas.
The Islamists have prohibited the mild stimulant, usually traded by women and mostly chewed by men in Somalia.
Pro-Islamist supporters have also held demonstrations in solidarity with the new leadership.
Ethiopian border 'closed'
The Islamists, who control the capital Mogadishu, now control most of southern Somalia and have nearly surrounded the headquarters of the internationally-recognised interim government, based in the provincial town of Baidoa.
Also on Saturday the Islamists said they had ordered the partial closure of the border with neighboring Ethiopia, accusing Ethiopian troops of invading, mining and shelling parts of Somalia's Hiran region.
"The border with Ethiopia is closed in the Hiran region for national security reasons," said Sheikh Hussein Mohamud Gagale, the Islamists' deputy regional security chief.
"Ethiopian soldiers are conducting military manoeuvers around Sarirale village, which is inside Somali territory," he told Mogadishu's Simba radio, noting that Sarirale is about 45 kilometers (28 miles) from the border.
"They also planted landmines around the border areas. The mines could kill our people and animals so we have taken the decision to block the border."
Addis Ababa immediately denied the claims.
"These are false allegations," Solomon Abebe, a foreign ministry spokesman, said.