The ship Rachel Corrie had ignored requests to change course prompting the boarding, Ynetnews.com reported Saturday.
An Israeli military spokeswoman said the crew complied.
"What happened today is the difference between peace activists and murderers," an Israel Defense Forces official said.
Israeli commandos stormed another humanitarian aid flotilla Monday, killing nine passengers -- eight Turks and one man of dual Turkish-American citizenship.
Autopsy results indicated all nine died of gunshot wounds and five of them had been shot in the head.
The Rachel Corrie is carrying hundreds of tons of aid, including wheelchairs, medical supplies and cement. Construction materials are banned from entering Gaza by Israel, which says Hamas could use them for military purposes.
Israel said the Rachel Corrie, carrying five Irish and six Malaysian activists, was being taken to the Israeli port of Ashod, where the cargo will be inspected.