The former-junta ruled nation boasts one of the largest armies in the world while a quarter of legislative seats are reserved for the military, giving them a de facto parliamentary veto.
Tens of thousands of soldiers are expected to take part in voting at military facilities ahead of the November 8 election, as they are scattered far from their home constituencies.
Observers from a 150-strong delegation will be allowed at polling stations in those highly-restricted bases after EU representatives met with powerful army chief General Min Aung Hlaing.
The decision "is going to make the vote more transparent and our report more accurate," he added.
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Holding an election in Myanmar is a Hercuelean challenge.
The impoverished country stretches from towering peaks in the north to southern tropical beaches, connected by poor infrastructure and blighted by myriad ethnic conflicts and the impact of recent devastating floods.
Then there is the added issue of a general lack of democratic awareness, with many people never having voted before in their lives.
"If we can't give them that kind of information," he warned, people like that would "lose their votes, their chances and their ability to change Myanmar," he said.
The EU is seeking to ensure the election passes freely and fairly after a flawed 2010 poll - boycotted by Aung San Suu Kyi's opposition - propelled the current quasi-civilian government to power.
Myanmar has been gripped by a colourful and boisterous election campaign, and the NLD are expected to make major gains.
But many NLD supporters fear the military's old habits will die hard and are on the look-out for signs of dirty-tricks in the poll run-up.
Concerns of mass disenfranchisement mounted after millions of the Myanmar diaspora working in neighbouring countries were not registered for advanced voting which began late last week.