Save the Children said two of its Myanmar staff were missing on Saturday, after the charred remains of more than 30 people were found, in an attack a monitoring group and local media blamed on junta troops.
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.
"People's Defence Forces" (PDF) have sprung up across the country to fight the junta, and have drawn the military into a bloody stalemate of clashes and reprisals.
On Saturday, photos appeared on social media purporting to show two burnt-out trucks and a car on a highway in Hpruso township in eastern Kayah state, with the charred remains of bodies inside.
A member of a local PDF group said its fighters had found the vehicles Saturday morning after hearing the military had stopped several vehicles in Hpruso after clashes with its fighters nearby on Friday.
"When we went to check in the area this morning, we found dead bodies burnt in two trucks. We found 27 dead bodies," he told AFP on condition of anonymity.
"We found 27 skulls," said another witness who did not want to be named.
"But there were other dead bodies on the truck, which had been burned to pieces so we couldn't count them."
Save the Children said later Saturday that two of its Myanmar staff had been "caught up" in the incident and were missing.
It added it had "confirmation that their private vehicle was attacked and burned out".
The two had been travelling home after carrying out humanitarian work in the region, the charity said in a statement, adding it had since suspended its work in several regions.
"We are horrified at the violence carried out against innocent civilians and our staff, who are dedicated humanitarians, supporting millions of children in need across Myanmar," chief executive Inger Ashing said.
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's junta previously said its troops had been attacked in Hpruso on Friday after its troops attempted to stop seven cars driving in a "suspicious way".
Troops had 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 on 24th December Hpruso township".
Satellite data also showed a fire had occurred around 1:00 pm (0630 GMT) on Friday in Hpruso, it added.
AFP was unable to confirm the reports surrounding the clash, but AFP digital verification reporters said the images purporting to show the incident had not appeared online before Friday evening.
PDF groups have surprised the army with their effectiveness, analysts have said, as the military struggles to break resistance to its rule.
Earlier this month the US said it was "outraged by credible and sickening reports" that Myanmar troops had seized 11 villagers, including children, in the Sagaing region and burned them alive.
Win Myat Aye, a member of a group of ousted lawmakers, condemned the atrocity.
"This is a cruel present from the military to our people on Christmas Day," he said.