The attack took place 11 nautical miles off the coast of Khan Younis, head of the Fishermen Committees in the Union of Agricultural Work Committees, Zakaria Bakr, told Ma'an news agency Thursday, presstv.ir reported.
Sources said at least four fishermen aboard the boats were detained, while Israeli forces confiscated some of the boats and towed them to an Israeli port.
Bakr identified the detainees as Khader Marwan al-Saidi, Muhammad Said al-Saidi, and brothers Haitham and Awni Tareq Bakr.
Further south in the Rafah port, an Israeli military vessel rammed into a Palestinian fisherman's boat, leaving him hospitalized and his boat damaged.
In recent years, Israeli forces have carried out more than a hundred attacks on Palestinian boats, arresting dozens of fishermen and confiscating some of the vessels.
Palestinians have held weekly protests near the Gaza fence over the siege on the enclave and the right for refugees to return to their homes they were forcibly expelled from during the 1948 creation of Israel.
More than 260 Palestinians have been killed by Israeli forces ever since anti-occupation protest rallies began in the Gaza Strip on March 30. Over 26,000 Palestinians have also sustained injuries.
The Gaza clashes reached their peak on May 14 last year, on the eve of the 70th anniversary of the Nakba Day (Day of Catastrophe), which coincided this year with the US embassy relocation from Tel Aviv to occupied East Jerusalem al-Quds.
The Gaza Strip has been under an Israeli blockade since June 2007. The blockade has caused a decline in the standard of living as well as unprecedented levels of unemployment and unrelenting poverty.
Israel carries out regular attacks on Palestinians in Gaza under the pretext of hitting Hamas targets. It has also launched several wars on the enclave, the last of which began in early July 2014 and ended in late August the same year. The Israeli military aggression killed nearly 2,200 Palestinians and injured over 11,100 others.