In the main city of Yangon, several thousand young people gathered at two sites to chant slogans, while hundreds massed peacefully in the second city of Mandalay, footage shown by a media outlet showed. "They aimed at our future", a young protester in Mandalay told the crowd.
"Lethal force, intimidation and harassment against peaceful demonstrators is unacceptable", UN Secretary-General Antonio Guterres said on Twitter. "It is like a sea of people", he said on the condition of anonymity. "That's why we come out to the front of the protests".
In addition to the dead, at least 22 people are reportedly injured.
The outbreak of violence was undeterred by demonstrators, with crowds assembling on Sunday in Mandalay and Yangon, the commercial center.
But if the numbers on Sunday are anything to go by, the violence looks unlikely to silence opposition.
Condemnation of the military also increases with United Nations special rapporteur Tom Andrews saying the new junta "can't steal the hope and resolve of a determined people".
In response to the violent crackdown by the military regime, the U.S. said that no one should be harmed for exercising their right to dissent, saying that it is "deeply troubled by the fatal shooting of protesters" in Mandalay.
Yesterday's death triggered a fresh wave of protest and anger.
USA state department spokesman Ned Price said the United States was "deeply concerned" by reports that security forces had fired on protesters.
Condemning the shootings, Mr Raab said: "The shooting of peaceful protesters in Myanmar is beyond the pale". On February 18, people living near Inle Lake, a popular tourist destination in southern Shan state, demonstrated against the military junta and demanded that democracy be restored in the Southeast Asian country.
Military spokesman Zaw Min Tun, who is also the spokesman for the new military council, has not responded to media attempts to contact him.
The trouble in Mandalay began with confrontations between the security forces and striking shipyard workers.
UN Special Rapporteur for Myanmar Tom Andrews said he was horrified by the deaths of the two, one of them a teenage boy. The shootings occurred near Mandalay's Yadanabon dock, where tear gas and rubber bullets were used on protesters earlier in the day. Inle Lake protesters welcome the sanctions and say that their goal is to end the military's dominance for good.
"Some of the aggressive protesters were also injured due to the security measures conducted by the security force in accordance with the law", the newspaper said without mentioning the deaths.
The demonstrators are demanding the restoration of the elected government and the release of Suu Kyi and others. She had been on life support after being shot in the head during protest in the capitol Naypyitaw.
Tension is expected to grow as her funeral is scheduled for Sunday.
The report said the 33rd Light Infantry Division led military operations in the village of Inn Din, where Reuters exposed a massacre of 10 Rohingya men and boys by soldiers and Buddhist villagers.
The army says one policeman has died of injuries sustained in a protest. The junta had seized power, baselessly claiming the landslide win for Suu Kyi'a party in a November election was the result of fraud.
The electoral commission had dismissed the fraud complaints.
"In line with our global policies, we've removed the Tatmadaw [the Myanmar military] True News Information Team Page from Facebook for repeated violations of our Community Standards prohibiting incitement of violence and coordinating harm", the platform said in a statement.
A rights group said 569 people have been detained in connection with the coup.