The German government has imposed restrictions on flights over southern Germany - the main approach to Zurich airport.
Swiss aviation authorities are warning that the new landing rules, which came into force on Thursday, could lead to passenger delays and increased noise pollution for nearby residents.
The restrictions follow last month's refusal by the Swiss parliament to ratify an aviation accord between Germany and Switzerland.
Unique, the operator of Zurich airport, said passengers had escaped delays on Thursday because sunny spring conditions had enabled use of a shorter east-west runway.
"There were no problems," said spokeswoman Sonja Zöchling.
But she did not rule out the possibility of delays in the future, particularly if bad weather closed Zurich's east-west "runway 28", which is unsuitable for larger aircraft in wet conditions.
Germany retaliated to the ditching of the aviation accord by banning aircraft from using the northern approach to Zurich airport - which lies 30 kilometres from the border - between 9pm and 7am.
Previously, aircraft could approach over southern Germany from 6am until 10pm.
Zöchling said the changes would affect about 30 flights a day, which would be redirected to runway 28 whenever possible.
The restrictions are set to toughen on July 10 when "out-of-hours" flights will only be granted permission to land from the north in poor visibility.
The limits mean major carriers such as the national airline, Swiss, could be forced to direct flights to Basel or Geneva.
Manfred Winkler, a spokesman for Swiss, told swissinfo it was impossible to predict which flights would be affected by the German decision.
"It depends on the weather and whether the runway is wet," Winkler said.
Flights most likely to be affected are Swiss's intercontinental services, some of which arrive in Zurich between 6am and 7am
These include flights from destinations such as Montreal, Sao Paolo, Rio de Janeiro, Africa and Hong Kong.
He added that Swiss had decided against issuing a general notification about the changes to passengers.
"For intercontinental flights from Asia, for instance, it would not be possible to know at take-off," Winkler said.
"[But] if we can't land in Zurich, then we would let passengers know that we'd be landing in Basel.
"We don't know which planes are impacted, so we don't want to unsettle passengers unnecessarily."
The new flight restrictions triggered the ire of the right-wing People's Party, which on Thursday condemned German action as discriminatory and damaging to neighbourly relations between the two countries.
The party called for retaliatory measures such as limiting the number of German heavy vehicles using trans-alpine crossings, as well as extra border checks for Germans entering Switzerland.
Zurich airport's increasing dependence on its eastern approach was criticised by communities living under the flight path.
However, the Federal Civil Aviation Office on Wednesday defended its decision to approve the use of runway 28, saying alternatives would have resulted in catastrophic disruptions at the airport.
The planned use of a southern approach to Zurich airport is at least 12 months away, because landing technology still has to be installed.
In addition, the southern option is likely to be further delayed by legal challenges from residents.
A southern flight path would cross Zurich's centre as well as the wealthy suburbs of Lake Zurich's northern shore.
swissinfo, Jacob Greber
Germany has limited the number of aircraft approaching Zurich airport over southern Germany.
From April 17, flights from the north will not be allowed between 9pm and 7am.
From July 10, Germany will no longer accept "technical exemptions" to the ban.
The Swiss authorities have approved the use of an eastern approach to Zurich airport.
But runway 28 is not suitable for heavy jets during wet weather.
Aviation analysts warn that in bad weather planes will have to be redirected from Zurich to Basel or Geneva.
Community groups have criticised increased use of runway 28 because of noise pollution.