Israeli leader Ariel Sharon has said the Gaza pullout is a painful step, but essential to secure Israel's future.
Settlers formed human chains to try to block the troops at Neve Dekalim
In a TV address, Mr Sharon insisted Israel could not hold on to the Gaza Strip forever and pledged full support for those settlers forced to leave.
He said Palestinians would now have to prove that they were committed to peace, and that if they did, Israel would offer an olive branch in return.
The first eviction notices were served to the remaining settlers on Monday.
About 9,000 people now have until midnight on Tuesday to leave Gaza's 21 Jewish settlements, and four of the West Bank's 120 settlements, or face forcible removal.
Riots broke out at the main gate of Alei Sinai settlement in north Gaza late on Monday after settlers heard rumours that they might be forcibly evacuated in the next few hours.
Groups of young settlers set tyres on fire in an effort to block the advance of the army, a BBC correspondent there reports.
Mr Sharon said the decision to pull out of Gaza had been painful for both him personally and the nation as a whole, but was unavoidable.
"We cannot hold onto Gaza forever. More than a million Palestinians live there and they double their number with each generation," he said.
"They live in uniquely crowded conditions in refugee camps, in poverty and despair, in hotbeds of rising hatred with no hope on the horizon."
Admitting that the withdrawal was a risky manoeuvre, he professed belief that it was undoubtedly the best way to ensure security and called on all Israelis to trust him.
He also gave a stark warning to Palestinians on how Israel would respond if they fail to crack down on extremist groups.
"The world is waiting for the Palestinian response... To an outstretched hand we shall respond with an olive branch, but we shall fight fire with the harshest fire ever," he said.
Mr Sharon was speaking at the end of a day in which Israeli troops handing out eviction notices in the Gaza Strip encountered defiant, but non-violent, resistance.
At Neve Dekalim, the largest Gaza settlement, the unarmed soldiers delivering the notices were confronted by protesters calling on them to disobey their orders.
The BBC's Richard Miron at Neve Dekalim says this is a highly emotional moment for both sides. Many protesters were in tears, along with a few soldiers.
Settlers spoke of feeling betrayed by the Israeli government's decision to evict them.
"I think that all this process is immoral, all this plan is just a disaster for us and when my government said it would find a solution for every settler, we find it a lie, because we are more than 600 families with no solution," Debbie Rosen, one of the residents at Neve Dekalim, told the BBC.
"We don't know where to go. We don't know where our kids are going to school and it is two weeks before 1 September and there's nothing prepared for us."
About half of Gaza's 8,500 settlers have already left. But those remaining have been joined by about 5,000 hardliners from Israel and the West Bank.
This is the first time that Israel has agreed to dismantle settlements built on Palestinian land seized in the Six-Day War in 1967.
Palestinian leader Mahmoud Abbas hailed the move as "historic" but said Israel should also pull out of the West Bank.
Hundreds of Palestinians marched through Gaza City to mark the start of the withdrawal and others headed for mosques to give thanks in a mass prayer meeting called by the militant group, Hamas.