The veteran democracy campaigner, who has suffered a bout of minor ill health in recent days, was conspicuously absent from the Armed Forces Day ceremony.
She has attended for the last two years since she entered a fledgling parliament set up under the quasi-civilian government that replaced junta rule.
"She needs to take as rest at this moment. That's why she couldn't attend the ceremony this morning in Naypyidaw," source close to Suu Kyi from her National League for Democracy (NLD) party told AFP, adding that she was "fine".
Suu Kyi's party is expected to sweep the elections, seen as a test of democratic reforms, if they are free and fair.
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But the Nobel laureate is currently barred from becoming president because of a provision in the junta-era constitution, which the military has resisted altering.
The election build up has coincided with rising fears that much lauded reforms in Myanmar are stalling, with recent police protest crackdowns fuelling concerns over the democratic transition.
Thousands of troops marched through an enormous parade ground backed by tanks, mounted missiles, fighter jets and airborne soldiers abseiling from helicopters on ropes.
Army senior general Min Aung Hlaing said in an address that this year's vote "represents an important landmark of democracy implementation".
But he added: "I want to say that any disturbances to stability of the state... Won't be allowed in the general election," according to an official translation of his speech.
In the same speech, Min Aung Hlaing cautioned against "too rapid" reforms, warning that they could cause "instabilities".
Nonetheless Myanmar's military remains deeply involved in politics four years after the end of outright junta rule and holds a quarter of parliamentary seats.