According to Ramadan al-Hayek, one of the organisers of the voyage, hundreds of people boarded over 30 fishing boats in support of the main vessel, said a report by Al-Jazeera.
In southern Israel, angry residents complained about the renewed rocket fire.
On Monday, the Israeli military killed a Palestinian it said approached the Gaza border fence with Israel.
"Israel will exact a heavy price from those who seek to harm it, and we see Hamas as responsible for preventing such attacks", Israeli Prime Minister Benjamin Netanyahu said.
Israel's Defense Forces (IDF) said three of its soldiers were wounded by mortar fragments on Tuesday, Haaretz reported. Egypt mediated the ceasefire reached in 2014, and have been instrumental in communicating between Hamas and Israel. Some were shot down by Israel's Iron Dome rocket interceptor system and others landed in empty lots and farmland.
It called on global agencies and human rights organisations to condemn the attack and punish Israel for its repeated crimes.
An Israeli tank drives along the border with the Gaza strip, on the Israel-Gaza border, May 29, 2018. The overnight Hamas rocket fire reached the city of Netivot for the first time since the 2014 war.
It was the largest barrage fired from Gaza targeting Israel since a 2014 war, and Israel's response would also be the biggest since then. It alleged some of the mortar rounds fired throughout the day were supplied by Iran.
"This is another wave of attacks by the IDF against the terrorist targets of the Hamas terrorist organization, which bears responsibility for all events in and from the Gaza Strip, as well as the severe attacks against Israeli citizens", said the IDF Spokesperson in a statement.
"Hamas [either] allows the fire to go ahead, turns a blind eye or is party to it. Hamas is not interested in escalation and yet allows the incidents to continue". Not mentioned are Egypt's closing of the Straits of Tiran to Israeli shipping, its ejection of United Nations forces, the amassing of Arab armies on Israel's borders, the declarations by Arab leaders' about Israel's impending demise, and the ongoing Syrian fire against Israeli communities in the north. Seventy-two people were killed on the Israeli side. Gaza's unemployment rate is edging toward 50 per cent, and the territory suffers from chronic power outages.
Israel has been condemned globally for its disproportionate use of force against the Palestinian protesters.
However, by now it has become clear that the Iranians want to keep up the pressure on Israel by attacking it from different fronts.
The UN Security Council is expected to meet Wednesday to discuss the attacks on Israel, following a request by the United States for an urgent meeting.