IDF naval forces made initial contact via radio with a pair of boats headed for Gaza – who refused to alter course.
The captains of the vessels were informed their course would lead them into waters legally closed by Israel and were informed they could turn around or head for a port in Egypt.
The passengers aboard the vessels - 27 activists from five countries - refused to heed naval instructions and continued on their course.
The Tahrir and Saoirse yachts set sail from Turkey on Wednesday saying they were carrying medical supplies.
The IDF has said it will not allow the boats to breach its blockade of the Hamas-terror organization in Gaza and is fully prepared for their arrival. Earlier this year a French vessel headed for Gaza was diverted to the port of Ashdod by IDF forces without incident.
Israeli officials also offered to unload any supplies aboard the boats and deliver them to Gaza. Israel allows hundreds of truckloads of aid supplies to enter Gaza via the Kerem Shalom, which is never at full capacity despite aid needs being met, every day.
Earlier on Friday flotilla organizers announced the activists aboard the vessels had pledged not to resist IDF naval commandos expected to board the vessels in order to redirect them to another port, probably Ashdod.
US officials previously warned their citizens not to participate in the flotilla. They also
US state department spokeswomen Victoria Nuland said the US had sought clarification of reports Turkish warships might be accompanying the flotilla and were told "quite emphatically" by Istanbul this was not the case.
"We've been clear to them that we think that would be an extremely bad idea and they've now reassured us that that is not what they are doing in this case," she said.
Turkey, whose prime minister Recep Tayyip Erdogan threatened to send a naval escort for Turkish vessels headed to Gaza, has stressed that the vessels are not flying the Turkish flag, and have no Turkish captains or passengers.
Erdogan's threat came after the release of the UN Palmer Report on the 2010 Mavi Marmara incident, during which 9 Turkish 'activists' who tried to lynch Israeli commandoes who boarded the vessel in accordance with international maritime law, were killed.
Turkey was incensed by the report, which concluded Israel's blockade of Gaza was "legal and appropriate."