"Egypt will not go to war with its brothers," Sisi said on state television, although Cairo fears its water supply will be affected by Ethiopia's Grand Renaissance Dam.
Foreign Minister Sameh Shoukry visited the Ethiopian capital last month for talks on the dam project on the Blue Nile.
Egypt relies almost totally on the Nile for irrigation and drinking water, and says it has "historic rights" to the river, guaranteed by treaties from 1929 and 1959.
"This is a national security need... You have military power to protect you, to protect this peace I'm talking about," said Sisi, himself a former armed forces chief.
"We always make sure that we stay within our borders, not conspire against anyone, not interfere in others' affairs," he said.
Sisi said his message was directed at Egyptians as well as "our brothers in Sudan and in Ethiopia so that the issue becomes clear for them".
Egypt is building a massive wastewater treatment and desalination plant to cope with potential shortages, the president said last week.
The Blue and the White Nile tributaries converge in Sudan's capital Khartoum and from there run north through Egypt to the Mediterranean.
The dam in Ethiopia is designed to feed a hydroelectric project to produce 6,000 megawatts of power - the equivalent of six nuclear-powered plants.
Ethiopia began building the dam in 2012 and was initially expected to commission it in 2017. But Ethiopian media reports say only about 60 percent has so far been built.
Khartoum says Halayeb has been part of its sovereign territory since shortly after independence in 1956, accusing Egypt of occupying it.
Last May, Sudan banned imports of Egyptian agricultural and animal products, and Khartoum recalled its ambassador from Cairo for "consultations" in January.
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