The hours-long meeting on Monday came after Kushner held rare talks with representatives of Hamas in Egypt over the weekend.
Netanyahu's office described the discussions as "deep and constructive" and said the two sides had agreed to establish two working groups, one focused on demilitarising the Gaza Strip and the other on sanitation, clean drinking water and other public health issues.
According to Israel, both sides agreed that demilitarisation should be completed "before any reconstruction" of the war-ravaged Gaza Strip begins.
There was initially no US account of the substance of the talks.
Kushner, who is US President Donald Trump's son-in-law, was accompanied by Nikolay Mladenov, a top official with Trump's Board of Peace.
On Sunday, Kushner discussed the future of the enclave with Egyptian President Abdel Fattah al-Sissi and representatives of Hamas in Egypt.
A little over a week ago, Netanyahu rejected the US-backed 15-point plan for the Gaza Strip drawn up by the Board of Peace.
Trump formally launched the body earlier this year, with overseeing the Gaza Strip's post-war transition among its main tasks.
"The Israeli military will not carry out any withdrawal until Hamas has been disarmed," Netanyahu said at the time.
He also reiterated his opposition to an independent Palestinian state.
Senior Hamas official Bassem Naim, by contrast, said Hamas remained committed to the Gaza roadmap.
Following Monday's meeting with Kushner, a senior Israeli government official said Hamas would be required to hand over all its weapons for destruction as a first step towards demilitarising the strip.
The process would be overseen by US General Jasper Jeffers, commander of the international stabilisation force currently being established, the official, speaking to reporters on condition of anonymity, said.
However, a fundamental disagreement remains over whether Hamas will actually disarm.
According to the Israeli official, Israel does not believe Hamas is ultimately willing to surrender its weapons while the United States believes this can be achieved.
Israel also continues to insist on its military retaining "freedom of action" to carry out targeted killings in the Gaza Strip, both in response to immediate threats and against militants involved in the October 7, 2023 attacks on Israel, the official said.
The official also said Israeli forces would not withdraw from the so-called "Yellow Line" when Israel's security was at stake, although it remained unclear whether Israel was ruling out a complete withdrawal in principle.
Under the Board of Peace plan, Israel, Hamas and other armed Palestinian groups would halt hostilities, with a transitional Palestinian administration backed by an international stabilisation force eventually taking sole control of the Gaza Strip's administration and security.
Weapons surrendered by Hamas would be stored under Palestinian control, with the process overseen by international monitors.
The plan also provides for a phased withdrawal of Israeli forces but the exact sequencing remains a major point of contention.
Israel has instead demanded the complete removal of weapons from the strip, arguing that they could otherwise eventually fall back into Hamas hands.
Trump, meanwhile, again suggested on Monday that he could intervene in Israeli politics by endorsing a candidate ahead of parliamentary elections in October in which Netanyahu is seeking re-election.
"I think it's most appropriate for me to stay out of Israeli elections, but I may endorse somebody," Fox News quoted Trump as saying in a telephone interview.
Trump called on Netanyahu to refrain from attacks in the Gaza Strip and said the United States maintained its own contacts with Hamas.
He said Hamas was "giving up their guns".
Turkish President Recep Tayyip Erdogan praised Hamas in an interview with al-Jazeera, saying the militant group was showing "genuine co-operation" and fulfilling its commitments.
