Sisi said their talks covered latest developments of situation after the U.S. President Donald Trump announced his country's recognition of Jerusalem as Israel's capital.
"Such a decision is threatening security and peace in the region," Sisi warned.
The Egyptian president told Putin about the importance of maintaining the legal status of Jerusalem within the international laws and the United Nations resolutions, applauding Russia's role in solving the Palestinian cause in the past decades.
On Syria, Sisi said they agreed on supporting the UN-sponsored negotiations to reach a political solution to the Syrian crisis.
He urged the international community to avoid creating any security or political vacuum in Libya.
Speaking about the anti-terrorism war, Sisi noted that he agreed with Putin to boost information exchange between the authorities in order to confront terrorism.
For his part, the Russian president described his talks with his Egyptian counterpart as "constructive and rich."
On Syria, Putin said he agreed with Sisi to enhance cooperation to boost a long-term solution in Syria, hailing Egypt's support to Russia's initiative for a national Syrian dialogue.
Addressing the Palestinian cause, Putin said Egypt and Russia were in favour of an immediate resumption of peace talks between the Palestinians and the Israelis to solve all thorny issues, including the status of Jerusalem.
Russia supports previous UN Security Council resolutions, said the Russian president, adding that all moves before the final results of peace negotiations are "meaningless."
Before their press conference, Sisi and Putin witnessed the signing of an agreement to build Egypt's first nuclear power plant.