Several people are said to have been hurt during the overnight operation in the city, where three pro-Russian protesters were recently shot dead.
Administrative buildings have been taken over by separatists in at least a dozen towns in eastern Ukraine.
Talks are reportedly taking place in Mariupol between the two sides.
In another development, the funeral is taking place of a pro-Ukrainian politician, Volodymyr Rybak, who was abducted and killed in the Donetsk region.
Meanwhile, President Barack Obama has accused Russia of flouting a deal on Ukraine reached in Geneva last week, under which illegal armed groups, including those who have seized public buildings, would return home.
Barack Obama told a news conference in Japan that Moscow had failed to halt actions by militants in the region and warned that the US had further sanctions against Russia “teed up”.
A contingent of US troops has begun landing in Poland for military exercises amid concerns among NATO’s eastern members about Russian intentions.
Moscow has said it will respond to any attack on its interests in Ukraine.
Unrest began in Ukraine last November over whether the country should look towards Moscow or the West.
Ukrainian Interior Minister Arsen Avakov announced on Thursday that the city hall in Mariupol, a port on the Sea of Azov in the Donetsk region, had been “liberated” overnight without any casualties.
“Civic activists” played a major part in the operation, he said.
According to the local news website 0629, a group of about 30 unidentified men in their twenties armed with baseball bats stormed the mayor’s office between 03:00 and 04:00 on Thursday.
The protesters called the police who reportedly came out and calmed down the opposing sides.
Negotiations are under way at the scene between the separatists, the local pro-Ukrainian authorities and the police, the site says.
While the interior minister said nobody had been hurt in the operation, 0629 reported that five men were injured, though not seriously.
Arsen Avakov also said that Ukrainian troops in Artemivsk, another town in the Donetsk region, had fended off an attempt by dozens of pro-Russian militants to seize weapons from a military unit. One soldier was wounded, he said.
Unverified footage of military helicopters, said to be flying over Artemivsk, was posted by a blogger on YouTube.
A local journalist, Anna Bokovaya, told Russian TV that about 50 people had taken part in the attack on the military unit, which lasted 45 minutes.
The militants began the attack after the soldiers inside rejected a demand to surrender, she said. The town was calm again on Thursday morning, she added.
Three pro-Russian protesters were killed when Ukrainian security forces fought off a raid on a base in Mariupol on April 17.
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