"We indicated several times to the organisers aboard the ship that they should head to the port of Ashdod as there is a blockade in force on the Gaza Strip, but they ignored our appeals and are continuing to head towards Gaza," a military spokeswoman said.
Earlier, a spokesman for the Gaza-based welcoming committee told AFP the Rachel Corrie had been intercepted and all communications with the ship had been cut.
"Several Israeli boats surrounded them between 30 and 35 miles off Gaza and prevented them from reaching Gaza," Amjad al-Shawa said after speaking by telephone with passengers on the boat.
In a last communique issued at around 5:38 am (0238 GMT), activist Jenny Graham, who is on board the Rachel Corrie, told organisers the vessel was being approached by two Israeli warships.
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Graham said equipment on board had been "jammed by the Israeli navy, and that they expected their satellite phone to be jammed soon as well," the Ireland Palestine Solidarity Campaign said, adding that it was not able to determine the ship's location when it was intercepted.
Israel had warned it would stop the Rachel Corrie -- a 1,200-tonne cargo ship named after a US activist killed in 2003 as she tried to prevent an Israeli bulldozer from razing a Palestinian home.
The vessel had been due to join a flotilla of ships which tried to run the blockade earlier this week but was held up for technical reasons.
Israeli naval commandos raided the flotilla before dawn on Monday in a bungled operation which left nine foreign activists dead, most of them Turkish, and scores wounded, among them seven Israeli soldiers.
