Projections showed centre-left candidates ahead in five regions but Renzi's party paid the price of internal divisions which split the leftist vote in Liguria, leaving a delighted centre-right to claim victory in the north-western region.
Sunday's polls were the first in recession-hit Italy since European elections a year ago, in which Renzi's Democratic Party (PD) stormed to victory with just over 40 percent of the vote.
While the premier's popularity remains high, the results were a warning of the threats he faces from a rise in leftist dissidents, anti-European and anti-immigrant sentiment, and the phantom of the billionaire Berlusconi.
Left scores own goal
"The League is the most serious alternative to Renzi in Italy today," its leader Matteo Salvini told Italian media after the anti-immigration party's candidate romped to victory over the PD in the Veneto region.
Political analysts singled out Salvini as the election's real victor, for winning over centre-right voters that had been seduced by Renzi.
But Berlusconi's centre-right Forza Italia party also had cause to celebrate.
The 78-year-old media magnate is keen on making a comeback after a series of legal woes which saw him forced to do community service for tax fraud.
His candidate Giovanni Toti looked set to snatch Liguria after the left scored an own goal by throwing a dissident PD, at odds with Renzi's centrist policies, into the ring.
La Stampa daily's political analyst Michele Brambilla warned that "those who had given Berlusconi up for dead got it wrong once again. Toti is his personal masterpiece, his creation... Berlusconi is still alive."
But Pippo Civati, who heads up the PD rebels, blamed his party's performance on its "shift to the right", which had seen it cost it support on both the left and the right "because (Renzi's) centrist model does not work".
Renzi had yet to comment publicly but was quoted by the Corriere della Sera daily as having told his inner circle the party would need to think long and hard about "loyalty" and "belonging to a shared political community."
Sporting a bitter smile, the paper said, he urged "respect for the rules and respect between all of us, for we're in the same boat."
Renzi not invincible
The PM had been relying on a strong result to show he has support for a series of unpopular reforms in the eurozone's third-largest economy, where unemployment remains near a 20-year high.
The FTSE Mib in Milan closed down 0.26 percent. Economy Minister Pier Carlo Padoan said the results "will not have repercussions either on the government or on the country's credibility."
Projections of the overall results in the seven regions showed Renzi's PD with 23.7 percent, ahead of the anti-establishment Five Star Movement on 18.4 percent, the Northern League on 12.5 percent and Forza Italia on 10.7 percent.
Senator Altero Matteoli of Forza Italia summed up the feeling on the right when he crowed that "a united centre-right can beat Renzi's left. This is the real lesson."
Others said a low voter turnout on a sunny bank holiday weekend -- ranging from 48 to 57 percent, depending on the region -- had saved Renzi from bigger losses.
"In the end, Renzi remains in the saddle, while the populist, anti-politics wave -- potentially destructive for the government -- dissolves into absenteeism," analyst Stefano Folli wrote in La Repubblica.
Nonetheless, "it is more difficult for Renzi to govern" now, because the results show he is not invincible, political commentator Marcello Sorgi said.