Jewish settlers had taken the Torah scrolls from the synagogues as well as prayer books and other holy items, symbolising the end of the use of the buildings as houses of worship.
On Monday morning, a giant bulldozer could be seen reducing to rubble one of the former places of worship in the evacuated settlement of Netzarim, just to the south of Gaza City, according to an AFP correspondent.
The synagogue had earlier been torched by scores of youths who had entered Netzarim shortly after the last soldiers left.
On Sunday, the Israeli government voted 14-2 to keep the former houses of worship intact, apparently in deference to Jewish rabbis who had ruled that the demolition of the buildings would constitute a violation of halacha, or Jewish religious law.
The Palestinian Authority (PA) called the Israeli decision "provocation" and "public relations entrapment".
The rabbis had warned the government that the destruction of the synagogues by Jews would send the wrong signal to the world and might precipitate attacks on Jewish houses of worship.
PA President Mahmoud Abbas on Monday dismissed the Israeli government decision as a public relations manoeuvre.
Hamas: Palestinian factions
agreed to destroy the structures
"They left empty buildings that used to be temples, but they removed all the religious symbols, and they are no longer religious places."
Earlier, PA National Security official Jibril Rajoub said the PA would demolish the empty buildings.
"These are not holy places. The Israeli army took away all holy objects, and all we have now is empty buildings, most of which are ramshackle," Rajoub said in an interview with Aljazeera on Sunday.
"These are symbols of the occupation. We don't need them, and we will dispose of them."
The PA said the synagogues were
'symbols of occupation'
Israeli officials denied the Palestinian accusations of provocation, saying the army left the synagogues intact because it "was too much to see Jews destroying Jewish synagogues".
Israel's Foreign Minister Silvan Shalom denounced the torching of the synagogues.
"This is a barbaric act by people who have no respect for holy sites. The Palestinians have taken no real effort to protect the synagogues," he told public radio.
Regev told Aljazeera.net that Israel was expecting the PA to do its utmost to respect and preserve the buildings.
When asked whether Israel would accept handing the buildings over to a third party or converting them into medical facilities for children, as was proposed by some foreign officials, Regev said Israel would welcome any solution that would respectfully deal with these structures.
Several Palestinian leaders had voiced concern over Israel's motives in abandoning the synagogues.
The pullout has ended 38 years
of Israeli military rule
"We are damned if we do and damned if we don't," PA negotiator Saeb Erikat said on Sunday during a radio interview with Israeli state-run radio.
He said Israel was adding "another sensitive problem" to those left unresolved by the withdrawing Israeli army, including the border crossings and the Gaza airport and harbours.
Israel and the PA are yet to reach agreement on these issues, which for Gazans could make the difference between a successful transition to political and economic freedom or remaining under Israeli control.
Rabbi Menachem Fruman of the settlement of Tku' near Bethlehem had proposed converting the synagogues into mosques, arguing that Muslims and Jews were worshiping the same God.
"We are damned if we do and damned if we don't"
However, some Palestinian leaders privately voiced fears that turning the synagogues into mosques could give Jews a pretext to pray at Muslim holy places, such as the al-Aqsa Mosque in Jerusalem.
"If we convert them into mosques, they would then demand the right to pray at the Aqsa Mosque on the grounds that since Muslims were allowed to pray in Jewish synagogues in Gaza, Jews also have the right to pray in the mosques," said one Hamas member from the Hebron region.
"We respect Judaism and other religions. But this is a media bluff. Hence the buildings should be demolished respectfully," Palestinian Authority Mufti, Ikrema Sabri, told Voice of Palestine radio.
The Hamas member, who identified himself as Abu Ahmed, said the demolition of synagogues by the Palestinians would also create problems.
"I think Israel wants the Palestinians to demolish these structures in order to have a pretext for some nefarious designs against Islamic holy places, especially in Jerusalem."
He said the PA should destroy the buildings immediately before they became an international issue.
A Hamas official in the Gaza Strip, Mahmoud al-Zahar, told Aljazeera.net in a telephone interview on Sunday that the synagogues would be demolished as soon as the Israeli army left Gaza.
The last Israeli soldier was due to leave the strip shortly before dawn on Monday.