5-Star had been hoping to build on its success a year ago, when it took charge of Rome after winning a landslide.
Right after voting ended late Sunday night, pollsters for both state TV and private TV said their samplings indicated the anti-euro 5-Star Movement would fail even to make runoffs in the four top races, including a big setback in Genoa, which is home to Movement founder, comic Beppe Grillo.
Substantial actual results were not expected until sometime Monday morning.
Until Grillo's Movement started gaining ground in the last few years, Italy's political scene had been dominated for a quarter-century by center-right coalitions, led by media mogul and former premier Silvio Berlusconi, and center-left alliances, now led by ex-premier and Democratic Party leader Matteo Renzi.
Despite its local difficulties, the most recent opinion polls taken ahead of Sunday's vote say the 5-Star would win more than 30 percent in a national race, just ahead of the ruling Democratic Party (PD) led by former prime minister Matteo Renzi.
The Five Star Moved hoped to build on these successes but its rule in the capital has been mired in controversy, denting its image, and its grassroots operations elsewhere have been snarled by internal feuding.
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Silvio Berlusconi's center right party and Matteo Salvini's right-wing Northern League have about 13 percent support. No Five Star candidate made the second round run-offs on June 25 in any of the major contests.
Yet the movement only managed to attain 20% of the vote or less in most of the main cities, which stood in stark contrast to the strong victories scored in Rome and Turin in May a year ago. Investors had said that a potential agreement on an electoral law was a negative given that a non-market-friendly party could win. He led the field on Sunday with the official 5-Star candidate trailing a distant fourth.
The only outright victor in a major city on Sunday was Leoluca Orlando, who led the centre-left to victory in the Sicilian capital Palermo, securing his fifth mandate.
In Rome, Five Star mayor Virginia Raggi also faced a series of resignations from her team and a colleague's corruption scandal.
The current legislature expires in 2018.
But the talks collapsed in acrimony on Thursday, meaning the election is likely to take place as scheduled early next year.