The car the abbot had been travelling in had no religious markings on it, according to the letter and had not slowed down at a checkpoint, leading junta troops to open fire.
An investigation would be carried out and the junta would take “action based on the facts”.
The abbot’s funeral would take place on Thursday
The military has long sought to portray itself as a protector of Buddhist identity, the majority religion in Myanmar.
Since seizing power in 2021 it has arrested and jailed locals and foreigners accused of “harming” Buddhism in its sweeping crackdown on dissent that has seen thousands jailed or killed, according to a local monitoring group.
But the clergy have also been at the forefront of political protests.
Huge demonstrations sparked by fuel price hikes in 2007 were led by monks, and the clergy also mobilised relief efforts after the 2008 devastating Cyclone Nargis and the inaction of a former junta.