However, in central and southern Italy Mr Renzi's centre-left Democratic Party (PD) fared better and ousted a right-wing governor in Campania.
The PD is trying to overhaul the labour market, education and the constitution, to galvanise the struggling economy.
Before the vote ex-PM Silvio Berlusconi became caught up in an election gaffe.
At a rally in Segrate, a town outside Milan, the centre-right Forza Italia leader asked someone for the name of the candidate, and then told people "vote Paolo," only to find out that Paolo Micheli was a leftist standing against his party and backed by the PD.
Sunday's elections involved seven of Italy's 20 regions, and there were mayoral contests in more than 700 municipalities.
The anti-immigration Northern League made gains beyond its Venice power base. The PD lost the Liguria region in the north-west to Giovanni Toti, who was backed by the League and Forza Italia.
Northern League candidate Luca Zaia secured a solid win in Veneto region.
The PD's performance was well down on the 41% it won in last year's European elections.
But in Campania, south of Rome, the PD's Vincenzo De Luca got nearly 40%, ahead of the incumbent centre-right governor.
The PD also won in Tuscany, Umbria, Marche and Puglia.
Italy's Rai News reports that PD took 23.7% of the vote in total, with the anti-establishment Five Star Movement second on 18.4%, then Northern League on 12.5% and Forza Italia on 10.7%.
Mr Berlusconi, 78, was prime minister three times between 1994 and 2011.
He announced plans for a political comeback earlier this year, after the country's highest court upheld his acquittal on charges of underage sex and abuse of office in March.
Local elections in Italy have delivered gains to right-wing parties in the north - a setback for Prime Minister Matteo Renzi's economic reform plans.