The Israeli army withdrew from Nablus on Tuesday but was back at dawn on Wednesday, witnesses said.
Bulldozers sealed off all entrances to the old city with rubble and jeeps patrolled the streets of much of the city to reinstate a curfew, they said.
About 50,000 people were confined to their homes.
The forces arrested the mother of one of the "wanted" Palestinians, Al Jazeera's correspondent reported.
Five suspects were previously arrested in house to house searches for militants, the army said.
The Israeli army said the operation is necessary since most of the suicide bombers trying to enter Israel from the West Bank come from Nablus.
Thus far, one Palestinian has been killed in the operation, which began on Sunday.
Plea for normal life
The ongoing Nablus incursion has been the largest Israeli military operation in the West Bank in months.
Adli Yaish, the mayor of Nablus, on Tuesday said the Israeli forces were gone and called on residents to resume their normal lives.
Municipal workers had already begun cleaning the streets in the raid's aftermath, the mayor said.
Soldiers continued to occupy some of the buildings in the city when the raid was suspended on Tuesday, Al Jazeera's correspondent said.
So far, Al Jazeera reports, quoting a Palestinian source, Israeli forces have failed to arrest any of the "wanted" activists of al-Aqsa Martyrs Brigades.
The Israeli army said a 42-year-old Palestinian man was killed on Monday when troops fired at figures moving on the roof of a building where they had seen armed men and where they later found a weapon.
Palestinians said he was unarmed and was shot from a passing jeep.
On Sunday, a small group of nervous Israeli soldiers forced a Palestinian youth to lead them into a home. The soldiers then took him, along with several young Palestinian men, into a military vehicle.
Israel's supreme court in 2005 had banned the practice of using Palestinian civilians as 'human shields' to search homes for explosives or fighters in advance of soldiers.
|Troops in about 80 jeeps, armoured vehicles |
and bulldozers raided the city on Sunday [AFP]
The army said troops arrested five wanted Palestinians on Sunday and uncovered workshops used to manufacture explosive devices and bomb belts, as well as a studio where suicide bombers recorded their farewell statements.
But Saeb Erekat, the Palestinian negotiator, said the offensive would "undermine the efforts" by Mahmoud Abbas, the Palestinian president, to maintain a ceasefire with Israel.
Ismail Haniya, the prime minister of the Hamas-run Palestinian government, condemned what he called "the criminal Israeli assault".