Senior General Min Aung Hlaing made the remarks at an annual display of military might by Myanmar's armed forces, a body that long crushed democratic aspirations with an iron fist but has since stewarded the country through a remarkable transition.
"I would solemnly impart the fact that the Tatmadaw (army) will cooperate to bring about the prosperity of the Union and its citizens," he said during a speech to troops at the annual Armed Forces Day parade in the capital Naypyidaw.
"Only if these two obstacles are properly tackled and overcome will there be advancement on the path to democracy."
Myanmar has undergone a stunning political transformation since 2011, blossoming from isolation under successive juntas to become an increasingly vibrant nation.
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Its growing political openness was crowned by a historic November election that saw Suu Kyi's National League for Democracy storm to victory.
After a lengthy transition her government will take over from the outgoing army-backed administration on Wednesday, ending more than five decades of direct and indirect military rule.
Her ability to cooperate with and confront the still powerful military will be a crucial test of her government, which faces a range of challenges including poverty, corruption, years of chronic under-investment and insurgencies by ethnic minority rebels.
The military still holds strong political sway under a charter that reserves a quarter of parliament seats for unelected soldiers and grants the army chief direct control over three key ministries: home affairs, border affairs and defence.