A Military Official said the deployment was routine but declined to say what operational duties the ships were performing. "I can confirm that there are 2 naval craft in the Red Sea. This is not unusual," the official told Reuters.
Homefront Defense Minister Matan Vilnai said Israeli Security Forces were on very high alert in the country's south and that Egyptian troops were acting against gunmen in the Sinai.
"There is a very specific alert that an Islamic Jihad organization wants to carry out an attack on the Egyptian border and we are taking this alert very seriously. It should be emphasized that the Egyptians are also acting," he said.
Militants killed eight Israelis in a cross-border attack on August 18 that Israel said had come from the Gaza Strip through Sinai. Five Egyptian security men were also killed when Israeli forces pursued some of the militants who had fled to Sinai.
Israel then killed 15 Palestinians in a series of retaliatory air strikes on the Gaza Strip, among them the commander of a militant group it blamed for the border assaults.
The two countries subsequently agreed that Egypt should boost its troop presence in the Sinai.
Egypt had long complained that restrictions imposed by its 1979 peace treaty with Israel made it hard to maintain security in the Peninsula.
In February, after Mubarak's downfall, two Iranian warships passed through the Suez Canal for the first time since the 1979 Islamic Revolution en route to Syria, a maneuver Israel described as "provocative".
Last month warships from Iran's fourth fleet completed a near two-month mission in the Red Sea and the Gulf of Aden, Iranian media reported.
Israeli warships are regularly stationed at a naval port in the resort city of Eilat at the northern tip of the Red Sea and patrol the area to the south as part of routine procedure to secure its borders.
The two ships were thought to have passed through the Suez Canal on their way to the Red Sea, although the Israeli military declined to confirm this. The only other way to get to the Red Sea would have been around Africa, a weeks-long voyage.
In June 2009 an Israeli Dolphin class diesel-powered submarine sailed the Suez Canal to the Red Sea as part of a naval drill, defense sources said, describing the unusual maneuver as a show of strategic reach in the face of Iran.
Each German-made Dolphin has 10 torpedo tubes, four of them widened at Israel's request - to accommodate, some independent analysts believe, nuclear-tipped cruise missiles.
But there have been questions about whether these would have the 1,500-km range needed to hit Iran from the Mediterranean.