According to the owner of the vessel, the Israelis destroyed its communication equipment and confiscated the phones of those on board.
The Israeli military told Al Jazeera it had captured the Lebanese vessel and taken it to Ashdod, where authorities were examining its cargo. The passengers and crew, meanwhile, were being questioned by police.
In a statement, the Israeli military said it had warned the ship on Wednesday night against entering Gaza's coastal waters.
"During today's morning hours, the cargo ship changed its bearing, and began heading towards the Gaza Strip .... disregarding all warnings made," it said.
|The Lebanese prime minister has condemned Israel's seizure of the aid ship [AFP]
, which originally set sail from Cyprus, left the Lebanese port city of Tripoli on Tuesday.
Maan Bashour, an aid co-ordinator for the group End the Blockade of Gaza, said the ship was carrying medical equipment, food supplies and books, toys and milk for small children.
"This ship was searched in Cyprus and in Lebanon," Bashour told Al Jazeera in Beirut, Lebanon. "And we were very eager to let it be searched by Lebanese and Cypriot authorities in order that there be no reason for the Israelis to prevent it from going to Gaza."
Foud Siniora, Lebanon's prime minister, condemned the attack on Al-Ikhwa, emphasising that it was on a humanitarian mission to Gaza.
"It is no surprise for Israel to perpetrate such an action as it has been accustomed to ignoring all international resolutions and values," he said during a speech in Beirut.
"I made a number of necessary phone calls with international parties in order to exert pressures on Israel which is violating laws. I hold Israel responsible for the safety of the ship and passengers. "