It follows a congratulatory video message by Ursula von der Leyen on Israel's Independence Day. In it she praised Israel, among others, for having made the desert bloom.
It has sparked an unusual diplomatic spat between the Palestinian Authority (PA) and the European Union (EU), its main donor.
A spokesperson for the commission told the BBC, "The EU is unpleasantly surprised by the inappropriate statement of the Palestinian foreign ministry accusing the president of the European Commission of racism."
The PA singled out Ms von der Leyen's suggestion that Israel had cultivated barren land, calling it an anti-Palestinian racist trope.
The
phrase making the desert bloom is commonly used by Israel and its backers to
describe what they view as the country's success in developing the land since
the founding of Israel in 1948.
However, Palestinians argue that it erases their history and suggests that the land was previously uninhabited or untended.
The PA is calling for an apology from the European Commission president.
"Seventy-five years ago, a dream was realized with Israel's Independence Day," Ms von der Leyen said in her message. "After the greatest tragedy in human history, the Jewish people could finally build a home in the promised land."
"Today, we celebrate 75 years of vibrant democracy in the heart of the Middle East, 75 years of dynamism, ingenuity and groundbreaking innovations. You have literally made the desert bloom, as I could see during my visit to the Negev last year."
The PA statement describes the message, addressed to Israel's President Isaac Herzog, as propagandist discourse and part of an ongoing dispossession of Palestinians.
The PA claims it "dehumanizes and erases the Palestinian people and falsifies their rich history and civilization".
In addition, it says that the European statement whitewashes Israel's occupation of lands Palestinians claim for their hoped-for future state and denies what they call the Nakba (Arabic for catastrophe) of 1948.
Some 700,000 Palestinians fled or were forced to leave their homes in the war that followed the Israel's creation.
Palestinians mark Nakba Day on May 15 according to the Gregorian calendar, while the timing of Israel's Independence Day follows the Hebrew calendar.
Some Palestinians on social media have also criticized or mocked the European leader for her comments about shared values with Israel.
The European Commission is part of the executive of the
European Union.
The spokesman for the commission stressed the EU's diplomatic ties with the PA,
pointing out that Ms von der Leyen met PA Prime Minister Mohammed Shtayyeh when
she visited the region in June 2022.
They said a meeting to co-ordinate the delivery of international aid to the Palestinians was due to take place in Brussels next week.
"The EU is actively looking for solutions for the difficult situation of the Palestinian people," they added.