Ibrahim Salah said his family was working in its field of olive trees west of Nablus when about 50 settlers descended on the area, some of them wielding metal bars and carrying guns.
He said his son, Basel, was hit on the head by rocks and taken to a hospital. Witnesses said four other people were lightly wounded.
Israeli troops arrived shortly after the incident and dispersed the crowd, evacuating Salah to a hospital, the army said.
The incident occurred near Havat Gilad, one of two dozen unauthorised West Bank outposts the Israeli government has pledged to dismantle.
Israeli settlements are illegal under international law, and US-led road map peace deal of 2002 called for a freeze on their construction.
Micky Rosenfeld, an Israeli police spokesman, said three Palestinians and one settler were lightly wounded in Wednesday's violence.
He said the farmers did not coordinate their work with the authorities, as is customary during the harvest season.
Repeated attacks by settlers in recent years have led the army to dispatch troops to protect the farmers during the harvest season.
The olive harvest this year is expected to yield a bumper crop, making it essential to the economic survival of cash-strapped Palestinians.
The Israeli newspaper Haaretz reported on Tuesday that Jewish settlements are expanding in the occupied West Bank in defiance of Israeli law, citing a government report.
The paper said the findings came from a secret government two-year study that came across "rampant construction".