Palestinian security sources and witnesses said Israeli troops pushed back into the northern West Bank town scacely a day after ending its four-month blockade.
Around 15 jeeps and tanks moved into the city and began surrounding several houses in the eastern sector, provoking clashes with Palestinian gunmen, they said.
The move comes barely a day after the army loosened its grip on the city, pulling troops out of the area overnight on Thursday. Troops had moved into Jenin en masse in mid-August following a bomb attack in Jerusalem.
But a military spokesman denied the operation was a fresh reoccupation of the city, saying troops were merely conducting routine searches.
"On Thursday we decided to remove the encirclement around the city but this doesn't mean that the force will not go back in to carry out patrols or conduct searches," he told AFP.
"Routine searches will be carried out and if necessary, arrests will be made," he said.
An Israeli military source said there was "nothing special" about Friday's activity.