"The referendum is not the end game. It is only a battle in this long struggle for the future of Egypt," said the National Salvation Front, the main opposition group. "We will not allow a change to the identity of Egypt or the return of the age of tyranny."
The opposition claims the new constitution seeks to enshrine Islamic rule in Egypt and accuses the Islamists of trying to monopolize power.
Critics say it does not sufficiently protect the rights of women and minority groups and empowers Muslim clerics by giving them a say over legislation. Some articles were also seen as tailored to get rid of Islamists' enemies and undermine the freedom of labor unions.
The opposition front said it filed complaints to the country's top prosecutor and the election commission asking for an investigation.
"The results of the referendum are for sure because of the rigging, violations and mismanagement that characterized it," the opposition group said.
However, the Brotherhood insisted violations were limited and should not affect the referendum's integrity.
The Freedom and Justice Party, the Brotherhood's political arm, said it hoped the passage of the constitution would be a "historic opportunity" to heal Egypt's divisions and launch a dialogue to restore stability and build state institutions.
If the violations are considered serious enough, there could be new votes in some areas that alter the results slightly.
One major concern in the aftermath of the constitutional turmoil is Egypt's deteriorating economy, which has been battered by the two years of turmoil and taken an added hit from renewed violence recently.
The referendum was conducted in two stages with the first vote on Dec. 15 and the second on Saturday. The Muslim Brotherhood and some media outlets have accurately tallied the outcome of past elections by compiling numbers released by electoral officials at thousands of individual polling stations shortly after voting closes.