WADA President Craig Reedie said the Board approved the recommendation by the Independent Compliance Review Committee that RUSADA remain non-compliant as two key requirements for reinstatement had still not been fulfilled.
"Having set a road map for compliance, there are two issues that have to be fulfilled and we can't walk away from the commitments," Reedie told reporters, adding that the RUSADA has made improvements.
Kuwait, Equatorial Guinea and Mauritius had also been found non-compliant by the Board, it added.
The decision is likely to add more pressure on the International Olympic Committee (IOC) to ban Russian athletes from the 2018 Winter Games, which are being held in Pyeongchang, South Korea.
Russia escaped a blanket ban at the 2016 Summer Olympics in Rio de Janeiro but remains barred from competing in international athletics events.
Yuri Ganus, director general of RUSADA, said the agency had done everything ii could to be reinstated apart from two criteria that had not been met and were out of its control.
"We fulfilled all the criteria that depended on us," Ganus told a news conference in Moscow. "There were two points that were beyond our prerogatives. Unfortunately they were not fulfilled."
Russian President Vladimir Putin has suggested the allegations were an attempt to sow discontent ahead of Russia's presidential elections.