Further seismic activity cannot be ruled out in the region in the coming days, the seismology department of the Zurich Federal Polytechnic School (EPFZ) said in a statement.
Experts "manually" recorded Saturday's quake at 5.30am at a depth of four kilometres near the city of St Gallen.
"The quake is probably directly linked to trials and stimulation activities during the drilling involved in a geothermal project at St Gallen, where several mini-quakes have already been recorded in recent days," the EPFZ statement said.
"The quake was widely felt in the region," it added.
Police said no damage had been reported.
The work has been temporarily halted, the Swiss news agency ATS reported.
The project, which began in March, is aimed at finding water at a temperature of 140 degrees Celsius nearly 4,500 metres below the surface to build a geothermal plant that would serve half the buildings of St Gallen.
Geothermal drilling in late 2006 and early 2007 in northern Switzerland near Basel caused a series of earthquakes, some greater than magnitude 3, leading to the scrapping of the project to build Switzerland's first geothermal plant.
The Swiss parliament voted in September 2011 to wind down the country's nuclear energy, unleashing a search for alternatives.
The last of Switzerland's five nuclear reactors is to be shut down by 2034.