Egyptian security officials arrested Ali on February 18 when he arrived at Cairo airport from one of several trips to Hong Kong, where he had meetings with his contacts, it added.
The statement named the Irishman as Brian Peter and the Japanese man as Shiro Izo.
They told Ali at one meeting in Hong Kong that they wanted him to work for their company from inside the Atomic Energy Agency, it said.
"The first accused [Ali] said that he understood from the course of this meeting that the company referred to was no more than a front for the activity of Israeli intelligence," it said.
Details sought on Egyptian reactors
The government statement said Ali's contacts were interested in information about the capability of the Inshas reactor, how many hours it operated, the type of experiments conducted with it, any technical problems with the reactor and reasons for them.
They also wanted to know how frequently the International Atomic Energy Agency (IAEA) inspects the reactor, it said.
Egypt's reactors are under IAEA supervision and the United Nations agency has had no serious complaints about Egyptian compliance with the nuclear Non-Proliferation Treaty.
Egypt dropped plans for nuclear power stations in the 1980s but the government last year announced plans to take another look at nuclear power as an alternative to fossil fuels.