He added that most of Tuesday's mortars had been intercepted by the Iron Dome missile defense battery but warned that the system was "still not hermetic".
Three Israeli soldiers were injured in Tuesday's barrages, two lightly and a third moderately, the army said.
The Palestinians have escalated the conflict in recent months after holding multiple, often violent, protests near the border between Israel and Gaza, prompting clashes between the Israeli Defense Force and Palestinians.
In a statement the group's spokesman said after Egyptian mediation a "ceasefire agreement was reached with Israel to return to calm".
A fragile truce appears to be holding on the tense Israeli border with the Hamas-ruled Gaza Strip.
Gaza's Hamas rulers said Wednesday they had agreed to a ceasefire with Israel to end the largest flare-up of violence between the sides since a 2014 war.
Islamic Jihad spokesman Daoud Shehab, acknowledging a ceasefire was in effect, said its success would depend on "whether Israel will refrain from any military escalation against Gaza".
Israeli cabinet minister Arieh Deri told Israel's Army Radio that he expected calm to be restored.
This follows weeks of Palestinian mass demonstrations near the fence with border.
At least seven Hamas and its allies bases were struck, security sources in Gaza said.
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US Ambassador to the UN Nikki Haley.
The majority of some 28 projectiles were intercepted by Israeli air defences and no injuries were reported.
Meanwhile, Kuwait on Tuesday circulated a watered-down draft UNSC resolution on setting up an global protection mission for the Palestinians in a bid to win European support in a vote expected this week, diplomats said.
The high Palestinian death toll in the border protests has drawn strong global criticism of Israel, with rights groups saying Israel's use of live fire is illegal because in many cases it has struck unarmed protesters who did not pose an imminent threat to Israeli soldiers.
One of the first places hit was a kindergarten near the Gaza border.
Israeli Prime Minister Benjamin Netanyahu has previously called for Indonesia to establish formal ties, and the Foreign Ministry revealed in 2016 that Israeli officials had been conducting secret meetings with contacts "in an attempt to improve the ties between the nations".
Israel unilaterally withdrew its settlements and military presence from Gaza in 2005. It said some of the mortars fired were supplied by Iran.
By late Tuesday, Israeli aircraft had hit 55 facilities belonging to militant groups in Gaza, including a cross-border tunnel under construction, in response to the Palestinian barrages, the military said.
Among the targets were rocket launchers designed for terrorism, a lathe for the manufacture of rockets and rocket engines, advanced naval weapons, military compounds, training camps and sites for the manufacture of weapons. They attacked in the morning as Israeli children were walking to school.
Israeli forces have killed at least 121 Palestinians in Gaza since weekly demonstrations started on March 30.