The report said 38 were killed in clashes near Rabaa al-Adaweya mosque in Nasr City in the capital Cairo; eight others were killed in Alexandria; and another one was killed in Fayoum, southwest of Cairo.
The police and Muslim Brotherhood (MB) have exchanged accusations over the responsibility for the deadly confrontations.
Earlier Saturday, however, the Muslim Brotherhood's Freedom and Justice Party said in a statement posted on its official website that at least 200 people were killed and more than 4,500 others wounded, most of whom suffered gunshot wounds, in confrontations in the Naser street in Cairo.
General Prosecutor Hisham Barakt ordered on Saturday forming a panel of prosecutors to conduct an investigation into the overnight bloody clashes.
The prosecution is currently counting the number of casualties, according to MENA.
Egyptian police spokesman Hany Abdel Latif said Saturday that the police "used no more than tear gas" in the clashes, denying that the police fired live bullets at protesters and claiming that Islamist protesters started the violence.
Also, the interior minister said in a press conference that the massive sit-ins by supporters of Morsi in Rabaa al-Adaweya Square in Cairo and Nahda Square near Cairo University in Giza "will be cleared in coordination with the armed forces in suitable time."
The hardline Al-Jamaa al-Islamiya group has slammed recent clashes and urged human rights organizations to condemn the criminal act.
The head of Nour Party, Younis Makhyoun, said that those who run the country are responsible for the bloodshed. "The perpetrators of these massacres should be brought to justice," Makhyoun added.
He called for forming a fact-finding committee comprising national figures to reveal the truth, adding that the current crisis can't be resolved by mobilizing rallies or by using violence.
The National Alliance for Supporting Legitimacy, which was formed from MB group and other Islamic forces before toppling Morsi, condemned in a statement what it claimed as a "massacre," and held the armed forces responsible for the violence.
The Alliance, which started a sit-in 28 days ago, stressed in a statement that it would continue the peaceful sit-ins.