Matan Vilnai, Israel's deputy defense minister, hinted during an interview on Israel Radio that Israeli forces had taken covert action to disable two of the ships that were supposed to have participated in the blockade-busting operation Monday.
Asked whether there had been an alternative to landing naval commandos on the leading ship, the Turkish-registered Mavi Marmara, before dawn Monday to prevent the flotilla reaching Gaza, Vilnai said: "All possibilities had been considered.
"The fact is that there were less than the 10 ships that were due to participate in the flotilla."
His remarks appeared to dovetail with the sudden breakdown of two of the aid ships, Challenger I and Challenger II, with mechanical problems at the same time as the flotilla gathered Friday evening off Cyprus.
They had sailed together from the Greek port of Heraklion on Crete. Both vessels experienced mechanical problems around 3:30 p.m. Friday as they approached Cyprus after a 30-hour voyage.
Challenger I started taking on water after its bilge pump broke down, said Greta Berlin, founder and spokeswoman of the Free Gaza Movement, which organized the flotilla of ships that sailed from ports around the Mediterranean for the rendezvous off Cyprus.
She said an inspection turned up "very suspicious faults."
Challenger II suffered steering problems and had to put into port in Turkish-controlled northern Cyprus to repair hydraulic lines.
It transferred its contingent of pro-Palestinian activists to the Mavi Marmara, which was subsequently attacked by Israeli naval forces in international waters off Cyprus as it led five other ships toward Gaza.
At least nine people, some of them Turks, were killed by gunfire from commandos of the Israeli navy's elite Flotilla 13 unit who said they were attacked by activists with clubs, iron bars and knives.
Berlin said that a third ship, the Irish cargo ship, MV Rachel Corrie, also suffered unexpected damage while en route to join the flotilla at the weekend.
The 1,200-ton vessel was named after a 23-year-old American peace activist who was crushed to death by an Israeli army bulldozer during a protest in Gaza on March 16, 2003.
Berlin said that inspections revealed that electrical wires had been tampered with but the group was awaiting the results of a fuller investigation.
She said the Rachel Corrie was being repaired and would sail for Gaza within two weeks. She declined to give the ship's location because of suspicions the Israelis were conducting sabotage operations.
Meantime, Israelis newspapers reported that an Israeli military officer, identified as Col. Itzik Turgeman, who briefed the Foreign Affairs Committee of the Knesset, on the deadly clash in the open sea, spoke of "gray operations" mounted against the aid flotilla.
He reportedly hinted that the engines of five ships were sabotaged by Israeli teams who "took care of them."
According to various published reports, no other details were available, apparently because of Israeli military censorship.
The Israelis have sabotaged Palestinian ships in the past. In 1988, frogmen planted limpet mines on a Greek ferry, the Solphrini, which sank in Limassol harbor in the Greek-controlled sector of Cyprus.
The vessel, renamed the al-Awda -- Arabic for "The Return" -- had been chartered in Athens by the Palestine Liberation Organization as a so-called Peace Ship to carry an international group of activists to Israel to dramatize the plight of Palestinian refugees. Israel was blamed for the sinking.
At the same time, three senior PLO officers were assassinated in a car bombing in Limassol by what official sources said were agents of the Mossad, Israel's foreign intelligence service.
Western intelligence operatives in Cyprus said at the time that three Mossad agents had arrived on the island two days before the bombing carrying what turned out to be forged Canadian passports.