Tensions have risen between Israel and the US, its top ally, over Netanyahu's handling of the war in Gaza.
US National Security advisor Jake Sullivan said later that Biden told Netanyahu Israel needed a coherent strategy rather than to smash its way into the war-torn enclave.
"A major ground operation there would be a mistake. It would lead to more innocent civilian deaths, worsen the already dire humanitarian crisis, deepen the anarchy in Gaza, and further isolate Israel internationally."
On Sunday, Netanyahu had reaffirmed his pledged to push into Rafah, in Gaza's southern tip where more than half of the territory's 2.3 million residents have been sheltering to escape fighting farther north.
However after Biden's call, the White House said Israel agreed to send teams to Washington to discuss the way forward and would not proceed with a Rafah operation before the talks happened this week or the next.
Meanwhile, Israel claims it killed 20 militants in a deadly clash at al-Shifa hospital in Gaza City early Monday.
In video from Israeli forces, Israeli soldiers could be seen firing their weapons and moving into the compound.
Gunshots and explosions were heard in eyewitness footage of the raid, which Israel says also resulted in the death of a top Hamas operative.
Israel says 'more than 200 terrorist suspects' were apprehended in Al-Shifa.
Gaza's Hamas-run health ministry said the Israeli raid led to multiple casualties and set off a fire in one of the buildings.
Fighting in Gaza continues to take a toll on civilians, cutting off food supplies for thousands.
A UN-backed monitor the Integrated Food Security Phase Classification, or IPC, said Monday around half of Gaza's population or 1.1 million people were facing "catastrophic" shortages of food.
And around 300,000 people there now face the prospect of famine-scale death rates.
