"I can confirm that at around 10:15 Central European Time, Estelle was attacked by five or six military vessels. Soldiers wearing masks were trying to board the boat," said Mikael Löfgren at Ship to Gaza to The Local on Saturday.
Löfgren told The Local that communication with the crew onboard the Estelle broke off shortly afterwards and telephone contact had not yet been re-established.
There are no reports of any violence in connection with the incident, which occurred in international waters.
"All I heard were voices that were not calm," Löfgren said.
Ship to Gaza is part of the Freedom Flotilla which aims to raise awareness by attempting to break Israel's sea blockade of the Gaza Strip.
Two years ago at the first attempt to reach Gaza by sea, a Turkish vessel in the flotilla was boarded by Israeli soldiers resulting in the death of nine activists.
Aside from its symbolic cargo or necessities, the Estelle is carrying a crew of 17 which includes nationals from Sweden, Canada, Norway, Israel, Greece and the US.
Löfgren told The Local that the embassies of the nationalities onboard the vessel have been informed and that the organization's lawyers had been contacted.
An Israeli government spokesperson has confirmed that the navy had contacted the Estelle and had been denied access, according to a report by Al Jazeera.
The spokesperson denied that the vessel had been boarded or attacked.
According to reports on shiptogaza.se the crew onboard the Estelle were contacted by the Israeli navy as they approached the Israeli coast on Saturday morning, some four hours from their destination Gaza City.