The charity said two of its staff members were among 30 people killed in Kayah state, where pro-democracy rebels have been fighting the military.
Save the Children has confirmed that two of its staff were killed in a Christmas Eve massacre blamed on junta troops that left the charred remains of more than 30 people on a highway in eastern Myanmar.
Anti-junta fighters said on Tuesday they found over 30 burnt bodies, including women and children, on a highway in Kayah state where pro-democracy rebels have been fighting the military.
Save the Children later said two of its staff members had been caught up in the incident and were missing.
On Tuesday the charity confirmed in a statement that the two men were "among at least 35 people, including women and children, who were killed."
"The military forced people from their cars, arrested some, killed many and burnt the bodies," it said, adding the two men were both new fathers.
"This news is absolutely horrifying," said chief executive Inger Ashing.
"We are shaken by the violence carried out against civilians and our staff, who are dedicated humanitarians, supporting millions of children in need across Myanmar."
Myanmar's junta previously said its troops had been attacked in Hpruso township on Friday after its troops attempted to stop seven cars driving in a "suspicious way".
Troops killed a number of people in the following clash, spokesman Zaw Min Tun told AFP, without giving details.
The Myanmar Witness monitor said it had confirmed local media reports and witness accounts from local fighters "that 35 people including children and women were burnt and killed by the military in the attack".
Satellite data also showed a fire had occurred around 1:00 pm (0630 GMT) on Friday in Hpruso, it added.
United Nations under-secretary-general for humanitarian affairs Martin Griffiths later said he was "horrified" by the reports and demanded the government conduct an investigation.
Save the Children, which has a staff of around 900 working in Myanmar, later said it had suspended operations in Kayah state and several other regions.
In October the group said its office in the western town of Thantlang was destroyed in junta shelling that also razed dozens of homes following clashes with a local anti-junta group.
Myanmar has been in chaos since the February coup, with more than 1,300 people killed in a crackdown by security forces, according to a local monitoring group.
Self-proclaimed "People's Defence Forces" have sprung up across the country to fight the junta, and drawn the military into a bloody stalemate of clashes and reprisals.