The board previously claimed they had not received the necessary documentation for adjustments and corrections made in the project's specifications, and thus denied it altogether.
The VNĪ now says the board had not properly evaluated the project and casts doubt on the legal basis of the decision to reject it.
The Museum of the Occupation of Latvia, built in 1971 to mark the 100th birthday of Lenin, is one of the most memorable historical buildings in Riga.
The museum has seen 25 years of independent Latvia, but renovation efforts have been limited.
Some prefer the museum to remain as it is, while plans have been in motion to add a white 'Future home' section to the building. Clashes between supporters of the two options escalated last year.