Sameh Fahmi and Mahmud Latif are accused of costing the state 714 million dollars in losses because of the deal, the sources said.
Five oil ministry officials will also stand trial on the same charges.
Fahmi and Latif, who was briefly oil minister earlier this year, are already in custody.
They are accused of "exporting gas to Israel at a price lower than international prices, harming public finances," the sources said.
The probe into the controversial deal has extended to ousted leader Hosni Mubarak himself.
Mubarak, who has been detained on suspicion of involvement in the deaths of protesters, was questioned about the contract earlier this week.
The 82-year-old former strongman is in police custody in a hospital in the Red Sea resort of Sharm el-Sheikh.
Local press reported that Mubarak denied having intimate knowledge of the negotiations for the 2005 agreement with Israel.
The state news agency MENA reported last week that Egypt's prime minister has asked for the revision of all contracts to supply gas abroad, including to the Jewish state.
Egypt supplies an estimated 40 percent of Israel's gas requirements.
Prime Minister Essam Sharraf "has directed the revision and review of all gas contracts Egypt agreed to with all countries, including Jordan and Israel," MENA said on April 13.
The contracts are to be revisited so the gas "would be sold with deserved prices that achieve the highest returns for Egypt," it added.
A sweeping probe into corruption has been launched under the ruling military council which took power when Mubarak was ousted on February 11 following anti-regime protests.
Several powerful members of the former regime and close associates are being questioned by prosecutors, including Mubarak's sons Alaa and Gamal.
- Follow Ynetnews on Facebook