Israeli security sources said the fighters were involved in making crude rockets and mortars for attacks against Israeli towns.
But Palestinian sources denied the Israeli claims, saying all of those arrested were ordinary citizens and not wanted by Israel.
Aljazeera's correspondent in Jenin said the Israeli forces started a military operation there at 2.30am on Monday.
Around 40 Israeli military vehicles raided the city and launched search operations. According to Aljazeera's correspondent, the Israeli forces arrested 10 Palestinians.
Armed clashes erupted later between Palestinian resistance fighters and Israeli forces, injuring a soldier, added the correspondent.
Israeli forces also launched an operation in the nearby Sahba village, arresting three brothers.
One Israeli soldier was injured in
clashes with Palestinian fighters
The raid on Monday was a rare invasion into a West Bank city by the Israeli military since Israel and the Palestinian Authority declared a de facto truce in February.
The army had said it would carry out only essential operations after the truce.
Israeli forces located a workshop last month on the outskirts of Jenin where they found components for crude rockets capable of being fired at the nearby Israeli city of Afula.
Israeli media said the resistance fighters arrested early on Monday were connected to the cell that had produced the rocket parts, adding the fighters were trying to produce munitions similar to the al-Qassam rockets that fighters in Gaza have regularly fired at the Israeli town of Sderot and Jewish settlements in Gaza.
Israel has already handed over two West Bank cities to Palestinian security control over the past month, but on Sunday delayed the transfer of Qalqilya because it said the Palestinians had failed to confiscate weapons from resistance fighters.
The delay was a setback for security cooperation agreed at a ceasefire summit last month.
Israel has not yet said when it would transfer control of Jenin.