"Fire balloons" had been prepared at one of the positions which had been hit, the statement added.
The Israeli military struck a vehicle belonging to the leader of the terror cell in Gaza that sends burning kites and balloons over the border to southern Israel, leading to arson fires that have destroyed thousands of acres of agricultural lands and woodlands.
The young Palestinians, in east of al-Bureij refugee camp in central Gaza Strip close to the border with Israel, were fired at when they were launching balloons carrying fire bombs into Israel, and two were moderately injured by the shrapnel of a missile, said the Health Ministry in Gaza.
The Israeli army's latest attack is believed to deter the flaming kites and balloons unit.
They also demand an end to Israel's decade-long blockade of the Gaza Strip, which has gutted the coastal enclave's economy and deprived its roughly two million inhabitants of basic commodities.
On Sunday, the IDF targeted a cell and vehicle in the Gaza Strip used for launching the incendiary devices, after several such attacks earlier in the day were said to have sparked a number of blazes that ravaged fields, nature reserves and nearly reached a military outpost.
Israeli troops have fired on the protesters, killing more than 120 Palestinians since the weekly demonstrations began on March 30.
According to Israel's Defence Minister Avigdor Lieberman, 400 kites have been intercepted from some 600 launched since the start of the recent protests.
"The alternative to kite terror is war", one official told Hadashot news on Sunday.
At least 130 Palestinians have been killed since the protests kicked off, of which at least 50 were identified by both Israel and Hamas as members of Hamas or other Gaza terrorist groups. The Israeli military says militants have endangered civilians by using the protests as cover to carry out attacks and to try to breach the border fence. "The Hamas terror organization is responsible for everything that happens in and from the Gaza Strip, and it will suffer the consequences".