Sharon said settlers who use violence - like the ones who pushed, shoved and cursed soldiers who demolished 11 abandoned homes in a seaside Gaza settlement earlier this week - were a minority among the 8000-9000 set for evacuation in August.
He also condemned calls for soldiers to refuse orders to evacuate settlers under a plan to withdraw from the Gaza Strip and four West Bank settlements.
"We all have to remember that the calls to refuse and to disrupt life in Israel endanger the existence of Israel as a Jewish, democratic state," Sharon said at an annual conference for the quasi-government Jewish Agency.
Defying Sharon's sharp words, a group of settler rabbis repeated their call for soldiers to refuse orders to evacuate settlers, issuing a statement that calls the Gaza withdrawal "immoral".
"Settlers have been acting as a parallel power to the Israeli government"
chief Palestinian negotiator
During Sunday's clash in the Gaza settlement of Shirat Hayam, Corporal Avi Bieber refused orders to participate in the house demolitions.
The army confiscated the US-born soldier's weapon and arrested him. Bieber faced a disciplinary hearing on Tuesday.
It was unclear whether the court would make a ruling in the closed-door hearing.
Chief Palestinian negotiator Saeb Erikat told Aljazeera.net the settlers were Sharon's creation in the first place so he now had to deal with the consequences.
"Settlers have been acting as a parallel power to the Israeli government. They have been attacking Palestinians, killing them, burning their fields and homes. It is about time that the Israeli government wakes up to them," he said.
David Ha'Ivri, chairman of the Revava Settlers Group told Aljazeera.net that violence was being instigated by Sharon and not by settler groups.
Israeli police are on high alert
ahead of a settler protest
"We are calling on Sharon not to use violence against any of our civilians. If he chooses to use violence our people will defend themselves. Sharon is threatening to destroy our homes and property, we will not be oppressed."
Israeli police were on high alert on Tuesday on the eve of a road block protest by ultra-nationalist settlers.
Police across the country were put on the second highest level of alert ahead of the new disruption planned for Wednesday, which was expected to include attempts to sabotage communication cables, and water and power lines.
A large number of settlers attacked Palestinian homes in the al-Mawasi area, surrounded by settlements, citizens told Aljazeera's correspondent in Gaza.
Residents of al-Mawasi cannot enter the area, south of Gaza Strip, unless they have special permits.
The settlers have destroyed contents of the medical clinic in the area, damaged citizens' farms and fired live bullets in the air, the residents added.
The settlers also raised Israeli flags on a number of Palestinian homes.
Ha'Ivri and his group – an organisation supporting Jewish national pride - are bringing in more people into the Gaza settlements that Sharon has earmarked for the August withdrawal.
"We are brining in more manpower, while Sharon's manpower is being reduced," he said.
"I think our move will be very successful. Half the Jewish soldiers sympathise with our agenda
and even the other half will find it difficult to follow orders to raise a hand against fellow Jews and drag them out of their homes."