The lethal crackdown came on Armed Forces Day. Senior General Min Aung Hlaing, the junta leader, said during a parade in the capital Naypyitaw to mark the event that the military would protect the people and strive for democracy.
State television had said on Friday that protesters risked being shot "in the head and back." Despite this, demonstrators against the Feb. 1 coup came out on the streets of Yangon, Mandalay and other towns.
The Myanmar Now news portal said 91 people were killed across the country by security forces.
A boy reported by local media to be as young as five was among at least 29 people killed in Mandalay. At least 24 people were killed in Yangon, Myanmar Now said.
"Today is a day of shame for the armed forces," Dr. Sasa, a spokesman for CRPH, an anti-junta group set up by deposed lawmakers, told an online forum.
Meanwhile, one of Myanmar's two dozen ethnic armed groups, the Karen National Union, said it had overrun an army post near the Thai border, killing 10 people - including a lieutenant colonel - and losing one of its own fighters.
A military spokesman did not respond to calls seeking comment on the killings by security forces or the insurgent attack on its post.
"They are killing us like birds or chickens, even in our homes," said Thu Ya Zaw in the central town of Myingyan, where at least two protesters were killed. "We will keep protesting regardless... We must fight until the junta falls."
The deaths on Saturday would take the number of civilians reported killed since the coup to well over 400.
"This 76th Myanmar armed forces day will stay engraved as a day of terror and dishonor," the EU delegation to Myanmar said. "The killing of unarmed civilians, including children, are indefensible acts."
News reports said there were deaths in the central Sagaing region, Lashio in the east, in the Bago region, near Yangon, and elsewhere. A one-year-old baby was hit in the eye with a rubber bullet.
In Naypyitaw, Min Aung Hlaing reiterated a promise to hold elections, without giving any time-frame.
"The army seeks to join hands with the entire nation to safeguard democracy," he said in a live broadcast on state television. "Violent acts that affect stability and security in order to make demands are inappropriate."
The military has said it took power because November elections won by Aung San Suu Kyi's party were fraudulent, an assertion dismissed by the country's election commission.
Suu Kyi, the elected leader and the country's most popular civilian politician, remains in detention at an undisclosed location. Many other figures in her party are also being held in custody.
RUSSIA 'A TRUE FRIEND'
In its warning on Friday evening, state television said protesters were "in danger of getting shot to the head and back." It did not specifically say security forces had been given shoot-to-kill orders and the junta has previously suggested some fatal shootings have come from within the crowds.
International pressure on the junta increased this week with new US and European sanctions. But Russia's deputy defense minister Alexander Fomin attended the parade in Naypyitaw, having met senior junta leaders a day earlier.
"Russia is a true friend," Min Aung Hlaing said.
Diplomats said eight countries - Russia, China, India, Pakistan, Bangladesh, Vietnam, Laos and Thailand - sent representatives, but Russia was the only one to send a minister.
Support from Russia and China, which has also refrained from criticism, is important for the junta as those two countries are permanent members of the United Nations Security Council and can block potential UN actions.
Armed Forces Day commemorates the start of the resistance to Japanese occupation in 1945 that was orchestrated by Suu Kyi's father, the founder of the military.
Gunshots hit the US cultural center in Yangon on Saturday, but nobody was hurt and the incident was being investigated, US Embassy spokesperson Aryani Manring said.
Protesters have taken to the streets almost daily since the coup that derailed Myanmar's slow transition to democracy.
General Yawd Serk, chair of the Restoration Council of Shan State/Shan State Army - South, one of the ethnic armies in the country, told Reuters in neighboring Thailand:"If they continue to shoot at protesters and bully the people, I think all the ethnic groups would not just stand by and do nothing."
Author and historian Thant Myint-U wrote on Twitter: "A failed state in Myanmar has the potential to draw in all the big powers - including the US, China, India, Russia, and Japan - in a way that could lead to a serious international crisis (as well as an even greater catastrophe in Myanmar itself)."