Alaa and Gamal Mubarak are accused of breaking stock market and central bank rules, state news agency Mena reported.
The case against them began in 2012, after their father was deposed the year before. The pair had been out on bail for the past three years.
The brothers - who deny any wrongdoing - will appear in court on 20 October.
The Cairo court also ordered the arrest of three others, and the defendants collectively face charges of embezzling 2bn Egyptian pound ($115m; £88m).
Both Alaa, 57, and Gamal, 54, are charged with embezzling at least 494m Egyptian pound after they decided to sell the National Bank of Egypt for profit.
Alaa is a businessman who stayed out of politics, while Gamal is a former bankerwho was widely viewed as being groomed to succeed his father before he was overthrown in the Arab Spring uprising in 2011.
The brothers were arrested at the time for a number of alleged crimes, and spent several spells in provisional detention.
Image captionHosni Mubarak, seen here in 2013, also spent time in prison
In May 2015, Alaa and Gamal Mubarak were sentenced alongside their father to three years in jail for embezzling at least 125 million Egyptian pounds from public money that was earmarked for maintaining presidential palaces.
Their sentences were covered by time already served.
The now 90-year-old former president, who ruled for three decades, was freed in 2017 after a court cleared him over of the deaths of protesters in the 2011 uprising.
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