Swiss Federal Railways (SBB) said technical problems with a tunnel were behind the delay in the completion of the Cornavin-Eaux-Vives-Annemasse (CEVA) line.
Work began in November 2011 on the 16-kilometre link, including a two-kilometre section in France.
But engineers encountered unexpected problems with the area along the route that runs beneath the Champel neighbourhood.
The terrain to be tunneled is less “cohesive” than expected and will require more reinforcements, CEVA’s project director Antoine da Trinidade told news media.
The holdup will not have any impact on the project’s budget, authorities say.
The biggest public transport project in Geneva was earlier held up by legal challenges mounted by residents of Champel.
Last week the French government agreed to financing a 234-million-franc share in the project.
The CEVA line is designed to make it easier to travel from Switzerland to Annemasse and other French communities on the south side of Lake Geneva, such as Thonon-les-Bains and Evian.
There is currently no direct train line between Geneva's main train station, Cornavin, and Annemasse.
As a result, thousands of workers living in France who work in Geneva drive into the canton, contributing to a growing traffic congestion problem in Geneva's city centre.