More than 200 people protested outside parliament in Rabat against the Jewish state's flag being hoisted at the COP22 conference that opened Monday.
"The Israeli flag at COP22 means Morocco symbolically recognizing the state of Israel. It's unacceptable," one protester told AFP.
"Death to America, death to Israel!" demonstrators cried while burning the Israeli flag and parading anti-Israel placards.
Several pro-Palestinian associations took part in the protest after calling on authorities to take action about the flag earlier this week.
On Tuesday, Morocco's Foreign Minister Salaheddine Mezouar responded that "UN meetings around the world welcome all nations" and that the fight against climate change "requires all governments to commit".
Morocco supported Palestine gaining observer status at the United Nations in 2012, Mezouar said, and is "the first to defend the Palestinian cause".
Mezouar denounced what he called "political exploitation" of the climate talks running to November 18.
In 2013, a film about Morocco's dwindling Jewish community caused a stir, with around 200 people—mostly Islamists—demonstrating against it being shown at the Tangiers film festival, denouncing what they called an attempt to "normalise relations with Israel."
The protests contrast with more cordial relations being established with a delegation of Moroccan journalists who arrived for a visit in Israel this week and were hosted by the foreign ministry despite the threats of intimidation they faced back home.