Greece's ruling conservative party New Democracy (ND) won local elections Sunday but was defeated in the capital of Athens and in the Thessaly region that was hard-hit by September's floods.
ND had already led in seven of 13 regions in last week's first round of local elections, which it increased to eight in Sunday's run-off votes.
But in Athens, the prime minister's nephew and incumbent ND mayor Kostas Bakoyannis lost to socialist candidate Haris Doukas.
A professor at the National Technical University of Athens, Doukas led with 55.93 percent while Kostas Bakoyannis 44.07 percent, with 90.51 percent of ballots counted.
In Thessaloniki, the second largest city in Greece, the ruling's party candidate, mayor Konstantinos Zervas, was also defeated.
In Thessaly, Greece's breadbasket region hit by a devastating summer storm that killed 17 people and destroyed crops, ND candidate Kostantinos Agorastos also lost.
Independent Kouretas Dimitrios had more than 59 percent of the vote with over 80 percent of ballots counted.
In Northern Greece, Apostolos Tzitzikostas, backed by the ruling party, won re-election in the first round to govern Central Macedonia for a third term with more than 60 percent of the vote.
There was a low turnout in Sunday's run-off votes, with turnout down more than 11.5 percent from last week's level of 42.6 percent, said Deputy Interior Minister Theodoros Livanios.
That, was "something that should concern us all", Prime Minister Kyriakos Mitsotakis said Sunday.
It was not a particularly good night for New Democracy, he conceded.
Four months ago, in the June general elections, ND enjoyed a landslide victory of 40.56 percent, 20 points more than its main rival, the radical left Syriza.
But the new government has faced criticism for its handling of the fires and floods that struck Greece this summer.