"The forces of the past do not allow us to work for future generations," Cerar told a press conference. "I am tendering my resignation."
Yesterday, the constitutional court invalidated the result of a referendum which approved a flagship government infrastructure project, the upgrading of transport links to Koper port on the Adriatic coast.
The referendum, held in September 2017, resulted in a vote in favour of the building of a new railway line to service the town, Slovenia's only major commercial port.
The constitutional court found that the government had not acted with due impartiality as it spent public money to back a yes vote for the scheme.
The ruling came amid a backdrop of a wave of public sector strikes over pay in recent months and ahead of parliamentary elections which are due in June.
Cerar said the ruling over the referendum was "the drop of water which made the vase overflow" for his fractious three-party coalition government.
Former law professor Cerar, 54, took office in 2014 when his SMC party scored a stunning electoral victory just one month after being created, having vowed to lead Slovenia back from the edge of economic crisis.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)