Fischer had planned to go to Brussels but was forced to hold a meeting by video link from Prague because of a problem with his plane, The New York Times reported.
The prime minister supports the treaty, which aims to make the union a more cohesive body. But Czech Republic President Vaclav Klaus is a skeptic and has refused to fly the EU flag.
Jose Manuel Barroso, the president of the European Commission, expects Poland to ratify the treaty this week, leaving the Czechs as the only holdout. Irish voters approved the treaty in a do-over referendum last week.
Swedish Prime Minister Fredrik Reinfeldt, who holds the rotating presidency, said Klaus has not yet accepted a telephone call from him. The Czech Constitutional Court is expected to announce next week whether it will hear a challenge to ratification by 17 senators.