Palestinian security sources said eight people were injured when a tank shell hit a house.
One of the boats was a Palestinian coast guard vessel believed linked to an arms-smuggling operation, the Israeli military said.
Israeli boats fired four missiles at the naval base, hitting a small patrol boat and a fuel tank.
Israeli military sources said a larger patrol boat, the Jandala, was destroyed with explosives planted by divers.
The attack came after the Palestinian Authority arrested two of three officials accused by Israel of involvement in an attempt to smuggle weapons into the territories on board a cargo ship.
Two of the suspects are believed to be Palestinian naval police officers.
The Israeli statement said the skipper and a senior officer of the cargo ship - the Karine A - had previously served on the Jandala.
'Tunnel found'
In other developments, Israeli tanks rolled into the town of Rafah, on the Egyptian border, where soldiers arrested eight Palestinians they accused of smuggling weapons.
A house which Israel said covered a tunnel used for smuggling weapons across the border was also destroyed.
Palestinian security sources said eight people were injured when a tank shell hit a house.
Bulldozers also continued to rip up the runway at Gaza International Airport, a key symbol of Palestinian aspirations for statehood.
The Palestinian Authority has denied any knowledge of the weapons-laden cargo ship, which Israeli forces intercepted in the Rea Sea on 3 January
However, it set up a commission of inquiry which accused three members of the authority - all previously implicated by Israel - of being responsible for the operation.
Two detained
On Saturday, Palestinian officials said they had detained two of the officials, while the third was still being sought.
The detentions have been welcomed by US officials, but greeted with scepticism by Israel.
"The arrest of certain senior members of the Palestinian Authority... is an attempt by Yasser Arafat to exonerate himself," said Raanan Gissin, a spokesman for Israeli Prime Minister
Ariel Sharon.
Israel says that Palestinian leaders, including Yasser Arafat, are behind the arms operation.
International reaction to Israeli actions against Palestinians has been mixed.
Spokesmen for UN Secretary General Kofi Annan and the International Committee of the Red Cross (ICRC) denounced the bulldozing of more than 50 Palestinian homes on Thursday and the tearing up of the runway at Gaza airport.
But US Secretary of State Colin Powell defended the airport operation as a "defensive action" to stop weapons falling into the hands of Israel's neighbours.
His comments were condemned by the Palestinian leadership.
Israeli operations began on Thursday with one of the most extensive demolitions to date in Rafah's refugee camp. More than 50 homes were destroyed and about 600 Palestinians left homeless.
Mr Sharon said he would not resume talks with the Palestinians until Mr Arafat arrested those behind violence against Israel.