The group hit the headlines in 2010 and 2012 when they attempted to ship in humanitarian aid from Sweden to Gaza. On both occasions 11 Swedish nationals were on board the vessels.
Famous Swedish author Henning Mankell was on board the 2010 voyage when the flotilla was attacked by Israeli commandos, according to Sweden's foreign ministry.
Two years ago another voyage was brought to a halt after Israeli soldiers surrounded and boarded the vessel named Estelle.
Prosecutor Henrik Attorps has launched the investigation into suspected criminal offences ranging from aggravated assault, aggravated unlawful threats, theft, and other crimes under international law which may have breached the Geneva convention.
"We have grounds to believe that such crimes were committed," the office of the public prosecutor said in a statement.
Members of the Ship to Gaza movement have welcomed the announcement.
"We don't know what the final outcome will be but it is very gratifying that it is being examined," Ship to Gaza's chairwoman Ann Ighe told Aftonbladet.
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.
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In 2010, in 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.