The slogans "Jews awaken" and "Stop assimilating" were scrawled on a mosque and another building in Jish, a small village in the Galilee just south of Israel's border with Lebanon.
Police said they were investigating the incident, which they condemned along with "all nationalistic hate crimes".
Jish council head Elias Elias told AFP that the tyres of more than 150 cars were punctured.
He said it was not the first time the mixed Muslim and Christian village had been targeted and asked what the reaction would have been if the place of worship defiled had not been a mosque.
"I can only imagine what would happen if things like this would have been sprayed on a synagogue in the US or Europe," he said.
"The whole world would be in an uproar."
The incident bore the hallmark of a "price tag" attack – a euphemism for Jewish nationalist-motivated hate crimes targeting Palestinians living in Israel and their property, as well as Muslim and Christian holy sites.
Prime Minister Benjamin Netanyahu "firmly condemned" the Jish vandalism and slogans, vowing to "find the outlaws and bring them to justice.
"We won't tolerate any attacks on our citizens," he said in a statement.
The head of the Palestinian-led Joint List, Ayman Odeh, condemned the attack and blamed the prime minister's rhetoric for stoking such hatred.
"For weeks Netanyahu is sending us one message – you're not wanted," Odeh said of Israel's Palestinian minority.
"Today we see the results."
Netanyahu has been accused of using anti-Palestinian rhetoric ahead of Israel's March 2 election, the country's third vote in a year.
Israel has seen a rise in acts of vandalism against Palestinians living in Israel in recent months, and in December, the tyres of 160 cars were slashed in annexed east Jerusalem.
Last month, Israeli police launched a manhunt after an apparent arson attack on an east Jerusalem mosque accompanied by Hebrew-language graffiti.