The Israeli prime minister’s office said President el-Sisi extended his deepest condolences over the loss of life and vowed to conduct a thorough joint investigation into the deadly shooting.
"The two leaders expressed their commitment to continue strengthening the peace and security cooperation that is vital to both countries," the statement read.
The shooting at the Israeli-Egyptian border in the Negev desert is one of the most serious incidents since the two countries signed a peace accord in 1979.
Egypt says a security officer pursued drug smugglers over the lines when he ran into Israeli soldiers, leading to a firefight. Israel says its soldiers were attacked.