"A man in his 50s died of tear gas asphyxiation after (Israeli) soldiers used tear gas against Palestinians at Qalandia," the ministry said in an Arabic-language post on its official Facebook page.
"He arrived dead to Ramallah hospital," it said, without naming him.
AFP journalists at the Qalandia crossing between the West Bank city of Ramallah and Israeli-annexed east Jerusalem said that Palestinians waiting to cross to pray at the Al-Aqsa mosque compound began throwing stones at Israeli security forces who responded with tear gas and sponge-tipped bullets.
The statement said that Israeli forces used unspecified riot dispersal means.
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It was the last Friday of the holy Muslim fasting month of Ramadan, when worshippers flock to Al-Aqsa for midday prayers.
A mosque spokesman said that 280,000 attended and he expected more in the evening.
Violence since October has killed at least 214 Palestinians, 33 Israelis, two Americans, an Eritrean and a Sudanese.
Most of the Palestinians were carrying out knife, gun or car-ramming attacks, according to Israeli authorities.