The power plant is being built by the Russian state corporation Rosatom at a reported cost of $30 billion, and will consist of four power units with a combined capacity of 4.8 gigawatts.
The two presidents were opening the construction of the fourth and final unit, according to Egyptian state media.
"The cooperation between our two countries continues and is developing. Egypt is a close friend of ours and a strategic partner," Putin said.
Egypt, which faces increasing power demand from a population of a 105 million, is seeking to position itself as a regional energy hub that exports electricity to neighbouring countries, and to diversify its energy sources.
Since Sisi became president in 2014 the country developed a surplus capacity for electricity generation but has been grappling with power cuts since last summer after heatwaves drove up demand for cooling.
Production of natural gas used for power generation has also been dipping, and Egypt resorted to burning more polluting fuel oil in some power stations as it tried to keep up LNG exports - an important source of scarce foreign currency.
"Introducing nuclear energy to the energy mix...is crucial to meeting the growing demand for electrical energy," Sisi said.
Moscow and Cairo signed an agreement in 2015 for Russia to build a nuclear power plant in Egypt, with Russia extending a loan to Egypt to cover the cost of construction.
Elsewhere, Russia is helping to implement projects to build Kudankulam nuclear power project in the Indian southern state of Tamil Nadu as well as Paks nuclear power plant in Hungary and Turkey's first nuclear power plant in Akkuyu.
Russian state nuclear corporation Rosatom also works in China and Bangladesh.
