Mayor Olaf Scholz was speaking to around 200 people at an old people's home in the Lokstedt area of Hamburg when the two activists jumped onto the stage.
Around 300 protesters had blocked the street in front of the building where the mayor was speaking, the Hamburger Abendblatt newspaper reported.
A handful of protesters also managed to get into the building and whistled as Scholz took to the stage.
Protests have been sparked by the treatment of the 4,500 illegal migrants living in the city.
Authorities have tried to round them up, while some are living in poor conditions in shipping containers and a church.
Scholz started speaking about the refugees when the two topless women jumped onto the stage.
"Lampedusa is everywhere" was written on their chests – a reference to the Italian island where a boat sunk on October 3rd killing around 370 refugees.
The women were forced off the stage by the mayor's bodyguards and taken away as the speech continued, the Abendblatt said.
While Scholz was speaking some of the refugees met in the city hall with politicians including parliamentary head of the ruling Social Democrats Andreas Dressel.
Referring to the protests Dressel said: “The question of the refugees will not be decided on the streets," the Abendblatt reported.
But protests are set to continue. On Friday a left-wing demonstration is planned before football club St Pauli play.
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