Yuriy Ganus has been removed as the Russian Anti-Doping Agency's (RUSADA) director general, prompting concerns over its independence from the Russian Olympic and Paralympic Committee.
RUSADA's supervisory board earlier this month recommended its founders - the Russian Olympic and Paralympic Committee - dismiss Ganus, advice that was taken on Friday.
Deputy director general Margarita Pakhnotskaya and the supervisory board's independent international expert member Sergey Khrychikov resigned this week.
RUSADA's non-compliance case is pending before the Court of Arbitration for Sport after it appealed the World Anti-Doping Agency's (WADA) four-year suspension of Russia from global sporting events.
WADA and the Institute of National Anti-Doping Organisations (iNADO) each responded to news of Ganus' removal with unease.
WADA, which previously said it was "extremely concerned" by the supervisory board's recommendation, said: "These developments reinforce the concerns expressed by WADA in its statement of August 5 in relation to the manner in which the founders reached the decision regarding Mr Ganus following a recommendation by RUSADA's supervisory board.
"[The developments] re-emphasise the critical importance for RUSADA to maintain its operational independence going forward.
"WADA is in contact with RUSADA and other relevant Russian authorities to get further clarifications on the latest developments."
It added: "It is a critical element of the World Anti-Doping Code that national anti-doping organisations, such as RUSADA, remain safe from interference in their operational decisions and activities in order to conduct their work independently and effectively.
"This is why the Compliance Review Committee made it a condition of RUSADA's reinstatement that WADA remains satisfied that RUSADA's independence is being respected and there is no improper outside interference with its operations."
iNADO said: "iNADO is deeply concerned by the control that the Russian Olympic and Paralympic Committee exercise over RUSADA.
"This was made evident today in the dismissal of Yuriy Ganus as director general by these two organisations."
It added: "It is a clear conflict of interest when sport organisations have the power to remove the head of a national anti-doping agency unopposed."