A statement from the Israeli leader's office said Jason Greenblatt "reaffirmed President Trump's commitment to Israel's security and to the effort to help Israelis and Palestinians achieve a lasting peace through direct negotiations."
Peace talks between Israel and the Palestinians have been frozen since 2014 and the Palestinians have been concerned at the more favourable approach shown by Washington towards Netanyahu since Trump came to office in January.
The statement added that during a conversation lasting more than five hours, Netanyahu and Greenblatt discussed Israel's settlement building "with the hope of reaching a formula that will aim to promote peace and security."
On Friday, Trump spoke to Palestinian President Mahmoud Abbas and invited him to the White House. It was the first phone call between the two leaders since Trump took office. Greenblatt is set to meet Abbas in the West Bank on Tuesday.
The Israeli statement added that "Greenblatt stressed how important enabling the growth of the Palestinian economy and improving the quality of life for Palestinians are to President Trump."
Before taking office, Trump named Greenblatt, his company's top lawyer, as his special negotiator for trade deals and other talks and his adviser to the Middle East and special representative for international negotiations.