The abandoned bag was discovered at 4.33pm when police cleared the platforms at the Cornavin station to allow a bomb disposal expert to deal with it, 20 Minutes reported.
But it turned out to be a false alarm.
Platforms 4,5,6,7 and 8 were closed until around 5.30pm when police lifted the alert.
Swiss Federal Railways (SBB) said the incident did not result in any major holdups on major Swiss lines.
However, a TGV to France was delayed by 50 minutes, while a regional train to the French border town of Bellegarde was half an hour late, 20 Minutes said.
Concerns in Switzerland have been heightened since the terrorist attack by jihadists in Paris on Friday that left at least 129 people dead.
On the weekend, the country stepped up presence at rail stations and French diplomatic buildings, and increased border controls between France and Switzerland.
Tailbacks as long as five kilometres have emerged at the Bardonnex border motorway entry point into Geneva from France during rush hours as a result of the extra checks.
Every weekday thousands of people living in France cross the border to work in Geneva or the neighbouring Swiss canton of Vaud.
Swiss Defence Minister Ueli Maurer, a member of the Swiss People's Party (SVP), and other SVP members have called for the army to reinforce Swiss borders.
But Swiss President Simonetta Sommaruga, a member of the socialist party, said it was not possible to systematically check everyone crossing the country's borders, broadcaster RTS reported.
“With the 750,000 people who enter our country every day, everybody knows that is not possible.”
Sommaruga, who doubles as police and justice minister, said Switzerland does not appear to eb a direct target of terrorists.
There exists no evidence of a link between the authors of the Paris attacks and Switzerland, she said.
And while the acts committed in the French capital were “unacceptable” it would be wrong to react in Switzerland with symbolic measures, she said.