The vandalism, reported by the 20 Minuten newspaper, occurred at a cafeteria where drinks were served before Rasmussen delivered a “Churchill” lecture, commemorating British statesman Winston Churchill’s commitment to a united Europe.
Riot police were on hand to prevent the situation from deteriorating and Rasmussen was not directly involved in the demonstration.
Protestors shouted slogans and brandished banners decrying NATO’s military activities in Afghanistan.
Rasmussen met earlier in Bern with Foreign Affairs Minister Dider Burkhalter and Minister of Defence Ueli Maurer.
They discussed cooperation between NATO and the Organization for Security and Cooperation in Europe, to be chaired by Switzerland in 2014.
In his speech to the university, Rasmussen championed the success of Europe, despite the current economic crisis.
After the tyranny and terror of the Second World War, Europe has experienced a period of unprecedented peace and prosperity, he said.
“We have transformed Europe’s tragedy into a triumph.”
Rasmussen also touted the role played by NATO in providing a “security umbrella” for European countries, including Switzerland.
He added that Europe is “now ready to play a bigger role in security matters”.