Germany imposed restrictions on some flights to the Swiss hub close to its border in 2003 after complaints from locals, clouding relations with its neighbour.
Bern will reduce its air traffic, Swiss Transport Minister Doris Leuthard told a conference on the sidelines of the World Economic Forum in Davos.
Leuthard and her German counterpart Peter Ramsauer signed a declaration of intention which will be formalised in an accord by the summer.
"Switzerland will reduce its traffic but we do not yet have the exact figures," ATS news agency quoted Leuthard saying.
Since Germany restricted flights over its territory planes have been forced to fly over highly populated areas south and east of Zurich.
Berlin acted after the Swiss refused to ratify an accord on the number of planes landing and taking off from the airport, whose flight path is about 20 kilometres from the German border.
In 2010 Switzerland took the row to the European Court of Justice, which ruled that the German measures were proportionate.