"Mubarak affirmed Egypt's rejection of any new offensive on Gaza," it said.
Senior Israeli officials have warned in recent weeks that Israel could launch another strike on Gaza, like the devastating 22-day war that ended in January 2009.
That offensive killed some 1,400 Palestinians, around half of them civilians, and 13 Israelis, 10 of them soldiers.
Following the war, the number of rocket attacks dropped significantly, although 230 rockets and mortar rounds were fired into Israel last year, the army said.
Israel's vice prime minister Silvan Shalom said last month that Israel would be forced to "respond with all our force" if Gaza militants kept firing rockets into the Jewish state.
The warnings were made against the backdrop of almost daily rocket attacks and retaliatory Israeli air strikes on Gaza.
Late on Wednesday, Israeli troops shot dead two Palestinians who were apparently trying to breach the border fence after a day in which militants fired seven projectiles, most of them mortar rounds, into southern Israel without causing casualties or damage.
Mubarak also warned the Israeli leader about the impact of a surge in violence on the deadlocked peace talks with Palestinian president Mahmud Abbas.
Direct talks between Netanyahu and Abbas stalled in September last year when Israel refused to renew a moratorium on settlement construction in the occupied West Bank.
The Palestinians have refused to continue talking while Israel builds on land they want for a future state.
The Egyptian leader stressed the need for Israel "to revisit its stances and policies, and to take tangible steps to build trust" with the Palestinians, MENA said.
A statement from Netanyahu's office described the meeting as "friendly and comprehensive."
Netanyahu highlighted the central role of Egypt in pushing forward the peace process and requested that Mubarak exert pressure on the Palestinians to return to "direct, intensive and serious negotiations," the statement said.
Netanyahu also updated Mubarak on the fence that Israel is building along the Egyptian border, aimed at stopping the influx of African illegal immigrants into the Jewish state.
One of the stumbling blocks to any peace deal is the rift between Abbas and Hamas, which ousted the Palestinian leader's Fatah faction from the Gaza Strip in 2007 and rejects any form of negotiations with Israel.
Israel and Egypt imposed a tight blockade on Gaza after Hamas seized power there, and since then, Egypt has failed in efforts to mediate a unity deal between the rival Palestinian factions.