On Friday employees of the museum - with its main building located inside a landmark Swedish-era tower in central Riga - released an open letter calling for the head of the museum to be replaced.
The letter, signed by 51 museum workers, representing three quarters of all employees, is addressed to Defense Minister Raimonds Bergmanis and media.
The Defense Ministry has overall responsibility for the museum - an arrangement which plays a role in the unfolding conflict.
The signatories' reel off a long list of complaints against museum director
The first complaint appears to be that museum director Aija Fleija - who has been at the museum for 25 years - is demanding the museum assert its independence from the commanders of the armed forces.
"We believe there now exists an insane situation in relations with the National Armed Forces (NAF) leadership. The Director is constantly stressing that in no case should a situation be allowed in which the NAF "impose their wishes" and that we are "independent museum and no one can dictate their rules to us."
By snubbing the NAF in this way, it makes it hard for museum employees to do their jobs, the letter maintains.
"Fleija's professional and ethical principles are only a declaratory slogan. The authoritarian, dominant management style that holds sway in the museum has contributed to the erosion of employees' initiative, reluctance to freely express creativity and a stressful working environment," it continues.
"Fleija's work and decision-making is largely based on emotion rather than logical reasoning or the collective opinions and suggestions of the Museum," it adds.
The Defense Ministry has said it will look into the concerns. Fleija rejects the criticism.