State comptroller Yossef Shapira, who is in charge of assessing state policies and the use of public funds, said in the report that Israel had not learned its lesson from the July-August 2014 Gaza war, when Palestinian groups fired thousands of rockets at the Jewish state.
The Israeli military believes the Palestinian Islamist movement Hamas which controls the Gaza Strip, and its allies, still have some of their arsenal and are also working to rearm.
In Lebanon, Israel estimates the powerful Shiite militant group Hezbollah has more than 100,000 rockets and missiles capable of reaching most of Israeli territory.
"Although the military has envisaged a scenario in which Israel would be the target of thousands, or even tens of thousands of rockets and missiles, it is doubtful whether it has adequate capacity to defend the country properly," media reports quoted Shapira's report as saying.
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The report says it was estimated in 2012 that 27 percent of Israelis -- more than two million people -- had no protection in the event of war.
But according to the comptroller, the figure was likely higher because some public shelters were unusable.
His report criticises the government for not having organised meetings on the protection and evacuation of civilians since the 2014 war. It also regrets that Bedouin communities in the desert within reach of rockets from Gaza have practically no protection.
In another chapter, it criticises the army for still not having provided a more effective early warning system for areas near Gaza, where residents during the 2014 war had just 15 seconds to find shelter.
That conflict killed 2,251 people on the Palestinian side, including 551 children, and 73 people including 67 soldiers on the Israeli side, according to the UN.
Shapira is also expected to submit in coming weeks the final version of an audit reportedly on Israel's lack of readiness in the face of the threat from tunnels used in 2014 by Palestinians to infiltrate Israel.