Turnout from two days of voting was around 67.63 percent from 78.9 percent in 2008, indicating widespread disillusionment with bickering politicians at a time of economic suffering.
Italy is seeing "a divorce with politics," commented the La Repubblica daily.
Aldo Cazzullo, a columnist for the Corriere della Sera daily, said the turnout figures reflected a "shocking discrediting of the parties".
Education Minister Maria Chiara Carrozza said the political world "has to do more to bring back disaffected citizens".
Analysts said the polls could put further pressure on Prime Minister Enrico Letta's fledgling government which was only unveiled last month after a two-month deadlock following nationals elections in February that left no clear winner.
But Reforms Minister Gaetano Quagliarello said it would be "perverse" to link the outcome of the polls to the future of the cabinet.
Early results indicated leftist challenger Ignazio Marino would win the mayoral race in the Italian capital against right wing incumbent Gianni Alemanno, although without an overall majority.
A second round run-off would be held on June 9th-10th.
Marino has criticized Alemanno over the city's traffic-clogged streets and a waste disposal emergency, as well as his failure to address the crisis triggered by Italy's longest recession.
Alemanno, a former neo-fascist, has defended himself by saying he inherited a badly indebted city hall from a succession of left-wing mayors.
Projections based on early results showed Marino winning with between 40.3 and 42.3 percent of the vote and Alemanno coming in second with 30.2 percent to 32.1 percent of the vote.
Marino, 58, is a former top transplant surgeon who has promised to improve public transport in Rome, clean up the city and pay allowances to young job-seekers to ease a worsening social crisis.
Nineteen candidates were running for mayor and voters complained of long and confusing ballots.
A total of 564 local authorities held elections, many of them facing a similar mix of problems – high debts, spending cuts and the challenges of dealing with the social fallout of austerity.
Analysts were paying close attention to the results as a bellwether of support for political parties and particularly the badly divided leftist Democratic Party, which failed to win an overall majority in parliament in February elections.
The coexistence of rightists and leftists in Letta's cabinet is uneasy and some analysts warn the government may only last a few months, especially if it cannot deliver quick results to ease the gloom from Italy's longest-ever recession.
Columnist Cazzullo said the grand coalition government was in fact "a coalition of weaknesses".
Meanwhile the anti-establishment opposition Five Star Movement led by former comedian Beppe Grillo, which captured a quarter of the vote in the February elections, has appeared to lose ground.