A statement said the talks with Russia's Foreign Minister Sergei Lavrov and Defence Minister Sergei Shoigu focused on "the struggle against terrorism" and bilateral cooperation.
Lavrov earlier discussed the situation in chaos-riddled Libya with his Egyptian counterpart Sameh Shoukry, the foreign ministry in Cairo said.
Rival administrations and militias have been fighting for control of oil-rich Libya since the 2011 NATO-backed uprising that toppled and killed veteran dictator Moamer Kadhafi.
Egypt's neighbour has also been a breeding and training ground for jihadists, including the Islamic State group.
The Cairo talks came after Egypt's air force on Friday bombed jihadist training camps in eastern Libya.
The air strikes were launched hours after masked gunmen shot dead 29 Coptic Christians in central Egypt, in an attack later claimed by the Islamic State group.
Forces loyal to east Libya military strongman Khalifa Haftar, which also took part in the strikes, said late Friday's raids hit a pro-Al-Qaeda group in the Libyan city of Derna.
"We hope Russia will do all it can so we can work together to eliminate terrorism," Shoukry said after meeting his Russian counterpart.
Egypt hopes "to continue its close coordination with Russia as part of political cooperation... but also security and intelligence cooperation to eliminate this phenomenon", he said.
In Libya, "the presence of terrorists and training camps that serve as departure points towards Egyptian territory is a direct threat to Egypt's national security," Shoukry said.
Sisi and his Russian visitors earlier "agreed on the importance of uniting international efforts in the battle against terrorism" and to step up their cooperation to meet that goal, the Egyptian presidency said.
A statement said Sisi told the Russian ministers that Cairo wants to bolster "economic, commercial and industrial ties" with Moscow.
Russia suspended all its flights to Egypt after the IS-claimed bombing in October 2015 of a Russian airliner carrying holidaymakers home from the popular Red Sea resort of Sharm el-Sheikh, killing all 224 on board.
Monday's talks also focused on the conflict in Syria.
Shoukry praised "Russia's role in the success of the Astana process" -- the talks in Kazakhstan trying to bring about peace in Syria -- and said he hoped it would lead to "a total ceasefire", his office said.
Earlier this month, Damascus allies Russia and Iran as well as rebel supporter Turkey signed a landmark deal to create four "de-escalation" zones across some of Syria's bloodiest battlegrounds.
Lavrov also met Arab League head Ahmed Aboul Gheit, with both men stressing the importance of "working seriously to find political solutions to the crises and armed conflicts in the Arab world", the 22-member bloc said in a statement.
The Russian ministers' visit to Cairo had been planned for weeks as part of regular meetings between the allied countries.