Blatter, 78, who heads the world governing body for football, had come to give a speech entitled “Football as the school of life” on the campus of Switzerland’s top university.
But hecklers cried “shit Blatter” in German and threw coloured smoke bombs outside the auditorium where Blatter was speaking, 20 Minuten newspaper reported.
Police appeared to restore calm but then a group of 100 demonstrators got inside the building in a bid to disrupt Blatter’s talk, the newspaper said.
However, the group was unable to find the access to the auditorium allowing officers the time to block entry to the facility.
The protesters eventually left, taking their protest into downtown Zurich where they disrupted the operation of trams, according to the report.
Fifa has courted controversy over bribery and corruption allegations linked to the awarding of the 2022 World Cup to Qatar.
Blatter, a Swiss sports administrator who has been president of the organization since 1998, has so far ridden out the scandals and vowed to seek a fifth term in office next year.
Etwas ungewohnter Anblick gerade in der ETH - wird wohl nicht nur Wissen sondern auch Sicherheit produziert ... pic.twitter.com/6mV2oZLEEy— Montaluna (@Montaluna) November 4, 2014