Justice Ministry said it would appoint judges to probe allegations of voting violations, including charges that some polling stations were supervised by court employees and not by judges, during the first leg of the referendum on December 15.
Also, the country's embattled prosecutor general Talaat Ibrahim Abdallah quit yesterday, just weeks after being appointed by President Mohamed Mursi.
Abdallah submitted his resignation to the head of the Supreme Judicial Council after growing demands from hundreds of public prosecutors asking him to quit.
The Council will examine Abdallah's resignation next Sunday, a day after a final round of voting in the referendum on Egypt's draft constitution. The first round of voting on the Islamist draft constitution took place on Saturday.
The prosecutor general was appointed by the president by virtue of a controversial constitutional decree that was issued on November 22. Though the declaration was later cancelled the prosecutor general remained in his post. He is known to be closely linked with the Muslim brotherhood.
Hundreds of judges and prosecutors had gathered at the prosecutor general's office yesterday after marching from the Judges' Club building, in protest of Mursi's decision to replace Mubarak-era prosecutor-general Abdel-Meguid Mahmoud with Abdullah.
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Representatives from the protesters met with Abdullah's deputy Adel El-Said but failed to reach a conclusion. Later El-Said presented Abdullah's handwritten resignation to the protesters.
Abdullah left his office shortly afterwards escorted by security forces. Protesters chanted in support of the decision, Ahram online reported.
Meanwhile, Egypt braced for opposition-backed mass protests in Cairo and elsewhere today over alleged polling violations during the first round of the referendum.
The National Salvation Front (NSF), the opposition coalition, urged Egyptians to "take to the streets on Tuesday to defend their freedoms, prevent fraud and reject the draft constitution".
It claimed "irregularities and violations" marred the initial stage of the referendum across half of Egypt.