World Anti-Doping Agency (WADA) Athlete Committee chair Beckie Scott has claimed she was "bullied" by Olympic Movement officials at the meeting which saw Russia controversially reinstated.
The Canadian told BBC Sport's Dan Roan that she was "disrespected" by members of WADA's Executive Committee in the Seychelles.
Scott resigned from the Compliance Review Committee (CRC) overseeing the potential return of the Russian Anti-Doping Agency (RUSADA) when it recommended that the scandal-hit nation should be allowed back.
This decision was rubber-stamped by WADA Executive Committee members who voted 9-2 in favour of reinstatement on September 20.
RUSADA had been non-compliant with WADA since 2015 when allegations of state sponsored doping in the country first emerged, but sporting officials from the Olympic Movement had pressed for this to be reversed.
This was granted despite two key criteria of WADA's roadmap for reinstatement not being met.
Scott, a former cross-country skier and Olympic champion who previously sat on the International Olympic Committee's (IOC) Athlete Commission, told BBC Sport that she felt "pressure" attending the Seychelles meeting.
"I would say I was treated with a level of disrespect and comments and gestures which were inappropriate," she said, before agreeing that they had tried to "bully" her.
"It was indicative of a general attitude of dismissal and belittling of the athlete voice at the table.
"There was laughter when I read the list of Athlete Committees who had produced statements and who were confronting the [Russia] decision.
"At the time it was upsetting, and on reflection it's a tactic, a manoeuvre and born out of a long-standing belief that athletes don't have to be part of this conversation."
The Olympic Movement representatives on the WADA Executive Committee are Italy's Francesco Ricci Bitti, Turkey's Ugur Erdener, Switzerland's Patrick Baumann, Czech Republic's Jiri Kejval and Slovakia's Danka Bartekova.
Russia has been accused of the systematic manipulation of the doping system at their home Sochi 2014 Winter Olympics, with the IOC forcing them to compete under a neutral flag at Pyeongchang 2018 in February.
The country remains suspended by the International Association of Athletics Federations and the International Paralympic Committee, but the IOC's ban on the Russian Olympic Committee was lifted immediately after Pyeongchang.
Russia had been asked to fully accept the McLaren Report, which outlined much of the evidence against them, and allow full access to the Moscow Laboratory before RUSADA could be allowed back.
A "compromise" deal was instead reached after the CRC claimed that a letter from Russian Sports Minister Pavel Kolobkov - which stated the country "fully accepted the decision of the IOC Executive Board that was made based on the findings of the Schmid Report" - satisfied the first requirement.
The Schmid Report largely substantiates the McLaren Report as it outlines the involvement of Russian Ministry officials in the state-sponsored doping scheme but its language is not as strong.
A "commitment" from Russia to provide data and access to the samples stored at the Moscow Laboratory via an independent expert met the second criteria, the CRC said.
However, the reinstatement has been met with outcry from various athlete groups and other bodies.
When resigning from the CRC, Scott said the decision was "unacceptable" for clean athletes.
WADA President Sir Craig Reedie defended the process, however, and said that ensuring access to samples and data was a key breakthrough after months of deadlock when Russia had refused to budge on the remaining criteria.
"I have a question for the athletes and that is what, in practice, is the alternative option?" the Scot said last month.
"There is a crucial element in what we have been doing and that is getting access to samples and data that will allow ongoing cases to continue.
"I am used to athletes complaining but I really want to know what their alternates are?"
Scott has now taken aim at Reedie and WADA director general Olivier Niggli, who she said did not step in to prevent her treatment at the Seychelles meeting.
"There was no confrontation or challenging of that behaviour at the time it took place," she said to BBC Sport.
"I think it's indicative of the leadership of WADA's alignment with the Olympic Movement."
In a statement sent to insidethegames, WADA moved to defend their position.
"Following some remarks made by Ms. Scott at the Executive Committee meeting last month, there was discussion among the members on a number of different topics and it is fair to say that during this stage of the meeting, tensions were running high leading to comments from all sides that reflected the strong views held," a spokesman said.
"However, the athletes' voice was clearly heard both through Ms. Scott and through the athlete member of the Executive Committee [Bartekova], who was sitting around the same table.
"Since the meeting, Ms. Scott shared concerns with WADA President Sir Craig Reedie and director general Olivier Niggli in a private letter to which the President has already responded stating that these concerns were being taken seriously.
"It is currently clear that strong and divergent views from different sections of the anti-doping community, as well as the public debate, do affect the tone and atmosphere of these meetings.
"Finally, the allegation made by Ms. Scott that WADA leadership is aligned with the Olympic movement is completely and demonstrably untrue.
"The leadership of WADA, including its President and Director General, are independent and have shown time and again that they make decisions exclusively in the best interests of the organiSation and the fight against doping.
"In fact, this independence has led to criticism of WADA leadership by the very bodies with whom Ms. Scott claims they are aligned.
"It is worth pointing out that the decision to reinstate the Russian Anti-Doping Agency was made following a recommendation by independent Compliance Review Committee and by a majority of the government representatives, not just those of the sport movement."
Travis Tygart, the chief executive of US Anti-Doping, has been among those to support Scott
"Today's BBC Interview with World Anti-Doping Agency Athlete chair Beckie Scott presents a damning and accurate reflection of the fragile state of the WADA-led global anti-doping system as it exists today," he said.
"It's appalling Olympic sport leaders would attempt to suppress athletes' voices as described by Beckie.
"The IOC tail is now unquestionably wagging the WADA dog, and that is not something anyone who cares about clean, fair sport wants to see."