The 62-year-old author of the Wallander detective series joined the flotilla from Cyprus by way of smaller boats "after almost 48 hours of playing hide-and-seek with Cypriot police," Ship to Gaza Sweden said in a statement.
After the ships were attacked and boarded on Monday morning by Israeli defence commandos reports indicate that at least 10 people were killed and dozens more injured.
Mankell is thought to have been one of the nine Swedes onboard the Sofia (Eleftheri Mesogeios) which was the last of the ships to be boarded. No contact has been made with any of the ships on Monday with all communications blocked and a full blackout imposed on all media reporting from the vessels.
The popular author, whose books about world-weary detective Kurt Wallander have sold more than 25 million copies worldwide and have been adapted to film and television, said last week that he was partaking in the flotilla to show his solidarity towards the Palestinian people.
"I think that when one talks about solidarity, one must always know that actions are what proves destiny," he told Sveriges Radio last Thursday.
"It is with actions that we prove we are ready to support something we believe is important," he said.
Among the other ten Swedes participating in the aid convoy including the theologian Ulf Carmesund, Jewish artist and musician Dror Feiler, Swedish Green Party MP Mehmet Kaplan, lecturer and author Edda Manga, and theology professor Mattias Gardell, the brother of Swedish comic Jonas Gardell.
It remained unclear on Monday afternoon whether any of them had been wounded in the attack as the first of the ships entered port.
Mattias Gardell was one of the two Swedes onboard the Turkish boat MS Mavi Marmara which is the one featured on film footage showing Israeli troops opening fire on the activists, according to the Svenska Dagbladet daily on Monday.
The Freedom Flotilla, carrying more than 700 passengers, were on the last leg of a high profile mission to deliver some 10,000 tonnes of supplies to Gaza as part of a protest against the three-year long blockade.
Israel had said the attempt to break the Gaza blockade was illegal and warned that it would intercept the ships and detain the activists before deporting them.
The besieged ships are all set to be towed to the Israeli port of Ashdod where the activists are due to be detained and foreign citizens deported to their respective countries, according to the Israeli defence forces.