For the remainder of the year, foreign taxis are restricted to one-way trips to the airport.
"We're very disappointed," said Claudius Marx, head of Germany's Hochrhein-Bodensee Chamber of Industry and Commerce, to newspaper NZZ.
Richard Seeber, an Austrian member of the European Parliament, was angered by the move.
"Ninety days will not even be enough to bring all the tourists to our region during the winter season," he told NZZ.
The new rules will come into force in the second half of 2012, said a statement from the Federal Council, giving taxi drivers enough time to conform to them.
The agreement, signed by the municipality of Kloten – where Zurich airport is located – the Canton of Zurich and the Swiss Confederation, is based on a treaty on the free movement of people between Switzerland and the EU, the statement said.
Outside of the 90-day limit, taxi drivers are authorized to make one-way trips to bring passengers to Zurich airport in accordance with transport treaties with Germany and Austria dating back to 1953 and 1958, which have previously been largely ignored, the statement said.