Palestine Solidarity Campaign protesters interruped a concert by the Israel Philharmonic Orchestra.
Boris Johnson condemned protests by the Palestine Solidarity Campaign last week, after the group interrupted a concert at the Royal Albert Hall last month.
Protestors twice disrupted the Israel Philharmonic Orchestra’s BBC Proms on 1 September and other audience members booed in response.
The Mayor said the performers did not deserve to be targeted in this way and the demonstrators should have faced legal action.
“It is disgraceful for any cultural event in London to be interrupted and I strongly deprecate it,” he said. “London is a city that supports cultural activities of all kinds.
“People have a right to come and perform here without having politics dragged into it and becoming subject to abuse they do not deserve.”
Mr Johnson added: “In an ideal world, anyone who abuses an orchestra and stops the enjoyment of a performance should be subject to prosecution.”
Several protestors in the hall shouted as Zubin Mehta was about to conduct Bruch’s violin concerto.
The Palestine Solidarity Campaign had previously called on the BBC to stop the concert from taking place.
The group claims on its website the Israel Philharmonic Orchestra shows “complicity in whitewashing Israel’s persistent violations of international law and human rights.”
The BBC cut off the coverage of the Proms during each interruption while security staff removed the demonstrators.