It said the 16-year-old was hit in the head during clashes with soldiers, and named him as Laith Abu Naim.
The ministry said he was shot in the village of Mugheer.
A spokeswoman for the Israeli military confirmed that "violent riots are taking place in this area and burning tyres and stones were thrown at the soldiers".
She said she was unable to confirm that any Palestinians had been hit by gunfire.
Nineteen Palestinians have been killed since US President Donald Trump's controversial declaration of Jerusalem as Israel's capital on December 6, most of them in clashes with Israeli forces.
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