Troops thrust back into Tulkarm and Bethlehem overnight, bringing to four - including Nablus and Qalqilya - the number of Palestinian-ruled towns again under Israeli occupation and sweeping curfews.
The operations are taking place against the backdrop of intense diplomatic efforts to kick-start peace talks, which have been off the agenda for nearly 18 months.
In the largest operation, in Nablus, Israeli troops continued house-to-house searches and patrolled the deserted streets for a second day.
Arrests were made in a residential area near al-Najah university, where many students live.
The army says hundreds of men have been detained for questioning during the operation in Nablus, particularly in the Balata refugee camp, although most have been released.
Up to 30 Palestinians were reportedly rounded up in Tamoun village, near Nablus, on Saturday morning after more than two dozen tanks and armoured vehicles entered the area and imposed a curfew.
A Palestinian boy was also wounded in the leg when soldiers opened fire to disperse stone-throwers during a search operation in the Faraa refugee camp, Palestinian witnesses said.
Conflicting views
Israel says the raids are meant to eradicate Palestinian suicide bombers before they can reach its cities, while the Palestinians say the hardline Israeli leadership is trying to further undermine their autonomy.
"This is Israel's message to the whole world, and proof they do not want to reach any agreement or any political settlement," Palestinian leader Yasser Arafat told reporters at his Ramallah headquarters.
Brief Israeli incursions began shortly after Israel wound up its massive offensive across the West Bank in April, which failed to scotch suicide bombings for more than a few days.
Israeli army spokesman Brigadier Ron Kitrey told Army Radio on Saturday: "It is very difficult to capture them at the entrance to cities, buses and restaurants and easier to try to catch them at their point of departure."
US diplomatic efforts
As part of efforts to break the deadlock, the head of America's Central Intelligence Agency (CIA), George Tenet, has begun a much-delayed visit to the region.
The main aim of his mission is to begin reform of Palestinian forces and to re-establish their security co-operation with the Israelis.
During a meeting with US envoy William Burns, Israeli Prime Minister Ariel Sharon emphasised "Israel's position that cessation of terror, violence and incitement and a thorough reform of the Palestinian Authority were conditions for progress in the diplomatic process", a statement from Mr Sharon's office said.
Mr Sharon also held talks on Friday with Osama el-Baz, an adviser to Egyptian President Hosni Mubarak.
Egypt is reported to have produced a blueprint for an overhaul of the Palestinian Authority which both Israel and the United States are demanding.
Mr Mubarak is due to travel to the US to meet President Bush next week.
The European Union has also been continuing its diplomatic efforts in the region, with foreign policy chief Javier Solana expected to meet Yasser Arafat on Saturday and Mr Sharon on Sunday.