According to eyewitnesses soldiers then opened fire and assaulted some fleeing protesters.
The incident, which was caught on camera, shows a speeding army truck crashing into the protesters from behind. People can be heard screaming: "The car is coming ... Please help! It hit the children ... Oh! ... Dead! ... Run ... run.”
The military said that they have arrested at least 15 people from the protest, and described them as “rioters”.
It has not commented yet on the use of a truck to ram protesters.
Two more anti-junta protests were held in Yangon later on Sunday despite the morning’s violence. Given the military's fatal clampdown on protestors, demonstrations are often held in small organised groups to minimise casualties.
At least 1,300 people have been killed since the 1 February coup and over 120 have reportedly died in custody. Since the Aung Sang Suu Kyi government was overthrown by the military, thousands of protesters have taken to the streets seeking the return of democracy.
Suu Kyi was on Monday found guilty on two of the 11 charges she faces, and sentenced to four years in prison.
The junta has justified the coup by alleging voter fraud in last year's general elections, which Suu Kyi won by a landslide. Independent observers have said the vote was largely fair.
On Sunday, the protesters had just begun the "flash mob" when within minutes the military descended upon them.
"I got hit and fell down in front of a truck. A soldier beat me with his rifle but I defended and pushed him back. Then he immediately shot at me as I ran away in a zig-zag pattern. Fortunately, I escaped," one protester told Reuters.
Another witness said that about five armed soldiers got out of the vehicle and chased after the protesters. "They opened fire and also arrested young people who had been hit by the car. At least 10 people were arrested," the person, who requested anonymity for fear of arrest, told the Associated Press.
A local news service, Myanmar Pressphoto Agency, announced that two of its reporters covering the march had been among those arrested. The agency said their photojournalist Kaung Sett Lin had been injured before being detained and they lost contact with TV reporter Hmu Yadanar Khet Moh Moh Tun.
The opposition's outlawed National Unity Government (NUG), a broad alliance of anti-coup groups that include members of Suu Kyi's ousted ruling party, said it was heartbroken to see peaceful protesters crushed to death.
"We will strongly respond to the terrorist military who brutally, inhumanly killed the unarmed peaceful protesters," the NUG said in a statement.
The United Nations, condemning the incident, has called for Myanmar to hold to account anyone using excessive force against unarmed civilians. "Those responsible for the use of excessive and disproportionate use of force against unarmed civilians must be held to account," Ramanathan Balakrishnan, the UN resident coordinator in Myanmar, said in a statement.
The United States embassy said it was "horrified" and supports "the right of the people of Burma to protest peacefully".
"We stand with the people of Burma in their aspirations for freedom and democracy and call on the military regime to end the use of violence, release those unjustly detained, and respect the will of the people," it said.
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