He said that the "majority of the deaths were caused by bullets and birdshots," adding that the identities of the dead were being ascertained.
Sunday's death toll was the highest in clashes between Islamists and police since several days of violence starting on August 14 killed more than 1,000 people, mostly Islamists.
In central Cairo, police fired shots and tear gas to disperse stone-throwing protesters. AFP correspondents saw several suspected demonstrators being arrested and beaten.
An interior ministry statement said police arrested 423 protesters in Cairo, accusing them of vandalism and "firing live rounds and birdshot".
Three months after Morsi's overthrow, followed by a harsh crackdown on his Muslim Brotherhood movement, the Islamists had planned to galvanise their protest movement in a symbolic attempt to reach Tahrir Square.
After several weeks of relative calm, the Islamists had said they would escalate their protests by trying to rally in the symbolic Tahrir Square.
Hundreds of thousands of people had filled the square in February 2011 to force president Hosni Mubarak to resign, and again in July 2013 to urge the army to depose his successor Morsi.
But on Sunday, security forces guarded entrances to the square, frisking people arriving for the anniversary celebrations.
Several thousand people, some carrying pictures of army chief Abdel Fattah al-Sisi, waved Egyptian flags as warplanes flew overhead in formation and patriotic songs blared from loudspeakers.
Sisi, flanked by interim president Adly Mansour and Jordanian Prime Minister Abdullah Nsur, attended a fireworks display in a military stadium, followed by a long song-and-dance show.
"The army, police and the people are together hand in hand...We will protect Egypt, the Egyptian people and the will of Egyptians," Sisi told the gathering amid loud cheers.
Earlier in Cairo, the air was thick with tear gas and the crackle of gunfire as police confronted several marches heading for Tahrir.
Prime Minister Hazem Beblawi urged Egyptians to unite, saying the country is on the road to recovery.
"As we go through these critical times all Egyptians should stand together, be confident and be optimistic about the future," he said in a televised address.
The Islamist Anti-Coup Alliance called for more protests this week and specifically urged students across Egyptian universities and schools to protest on Tuesday "against these continuing massacres".
"The alliance holds coup authorities and the military-appointed government fully responsible for all the blood of Egyptians being spilt right now, and for every Egyptian killed on this day," it said in a statement.
Morsi's opponents demonstrated in their millions in June and July to urge the army to remove him, accusing the Islamist of failing the revolution that brought him to the presidency and concentrating power in the hands of his allies.
Interior ministry warning
His supporters decried his overthrow a year after his election in Egypt's first free polls as a violation of democratic principles.
Away from the main squares, Cairo's streets were largely deserted on Sunday, a public holiday to commemorate the October War, known as the Yom Kippur War in Israel.
The conflict, remembered proudly by the Egyptian army because it caught Israel by surprise, led to the recovery of the Sinai Peninsula in a 1979 peace treaty.
The interior ministry had warned it would "firmly confront" any violence or attempts to disturb Sunday's celebrations, state news agency MENA reported.
Attempts by Islamists to reach Tahrir on Friday sparked clashes with Morsi opponents and security forces that killed four people.
Analysts called the Islamists' call for protests a high-risk attempt to strip the current high command of the army's legacy and patriotic pride in the Arab-Israeli conflict.
"They will try to show that the present army is not the army of all Egyptians, but only of those who backed the coup," Hassan Nafaa, political science professor at Cairo University, told AFP.
"But this message will not go down well."
The Anti-Coup Alliance's ability to mobilise large numbers in its demonstrations has waned as security forces have arrested some 2,000 Islamists, including Morsi himself and several Brotherhood leaders.
Hundreds were killed on August 14 when security forces moved in to destroy two large pro-Morsi protest camps in Cairo, and ensuing clashes in the following days.