Lewis Hamilton says the actions of Formula 1's governing body have been "unacceptable" in launching an inquiry into Toto and Susie Wolff.
The FIA on Thursday ended a conflict-of-interest investigation into the married couple - just two days after it began.
Hamilton said it was "disappointing" the FIA had "sought to question the integrity of one of the most incredible female leaders we've ever had in our sport".
He said it had done so "without questioning [her], without any evidence".
Hamilton did not directly reference Toto Wolff in his remarks, but he was also referring to the allegations against his team principal, who he had praised in an answer to an earlier question.
The seven-time world champion's comments, made in a news conference before the FIA's end-of-season prize giving gala in Baku, came after Mercedes made it clear they were considering all legal options.
Mercedes issued a statement from Toto Wolff on Friday saying the team were "in active legal exchange with the FIA" .
It said Mercedes "reserved all legal rights" and wanted "full transparency about what took place and why".
The statement can be interpreted to mean that Mercedes is seeking full redress from the FIA - including a retraction of all allegations, a statement saying it did not mean to damage the reputation of the company or Wolff, and a full apology.
In a separate statement, Susie Wolff described the FIA's behaviour this week as "simply not good enough", adding: "As a sport, we must demand, and we deserve, better."
Wolff - the managing director of the F1 Academy, a category for aspiring female drivers - said: "I intend to follow up until I have found out who has instigated this campaign and misled the media."
The FIA has so far failed to respond to OceanNewsUK requests for comment.
Hamilton also questions FIA on sustainability
Hamilton said the FIA's actions this week illustrated a disconnect within its leadership on the subject of diversity, although he did not mention anyone by name.
The 38-year-old said: "They have a lot of great people in the sport doing amazing work and there is a constant fight to really improve diversity and inclusion within the industry.
"But it seems there are certain individuals in the leadership within the FIA that every time we try and make a step forward they try to pull us back, and that has to change.
"This is a global sport and we have such an incredible opportunity and a responsibility to be leaders of change.
"I want to acknowledge that there are a lot of people who are doing great work. But we need some change to make sure we are all pushing in the right direction."
He also questioned the FIA's decision to hold its gala in Azerbaijan, saying it undermined the organisation's claims to be promoting sustainability.
"There is a question in my mind whether the FIA is I really thinking actually about sustainability when so many people flew out here but the FIA is in Paris and it would have been easier to have it there," Hamilton said.
What is the row about?
The statements by Hamilton and the Wolffs are the latest developments in an extraordinary saga that has engulfed the FIA and its president Mohammed Ben Sulayem this week.
It started on Tuesday when the FIA said an "allegation of information of a confidential nature being passed to an F1 team principal from a member of FOM (Formula 1 Management) personnel" had been passed to its compliance unit.
It did not name the Wolffs, although it was referring to them.
The statement followed a magazine article alleging rival teams had complained to the FIA about confidential information potentially passing between F1 and Mercedes through the Wolffs.
But on Thursday the FIA said it was "satisfied" F1 had measures in place to protect against such issues, adding that there was "no ongoing investigation" on the subject.
In the two days between the inquiry starting and ending, Mercedes and F1 had issued statements rejecting the accusations and making clear their frustration with the FIA's handling of the matter.
And the nine other F1 teams all issued co-ordinated and identically worded statements saying they had had made no complaints to the FIA of this kind and that they were "pleased and proud to support F1 Academy and its managing director".
On Friday, Susie Wolff said in a statement on social media: "When I saw the statement issued by the FIA yesterday evening, my first reaction was: 'Is that it?'
"For two days, insinuations have been made about my integrity in public and through background briefings, but nobody from the FIA has spoken to me directly.
"I might have been collateral damage in an unsuccessful attack on somebody else, or the target of a failed attempt to discredit me personally. But I have worked too hard to have my reputation called into question by an unfounded press release.
"We have come a long way as a sport. I was extremely thankful for the unified support of the F1 teams. I have worked with so many passionate women and men at F1 and the FIA, who have the very best interests of our sport at heart.
"However, this episode has so far taken place without transparency and accountability. I have received online abuse about my work and my family.
"I will not allow myself to be intimidated and intend to follow up until I have found out who has instigated this campaign and misled the media."
Mercedes' statement concluded: "We ask for your understanding that we will not be commenting officially for now, but we will certainly address the matter in due course."
A damaging episode for the FIA president
The saga has left senior figures in F1 questioning the judgement of Ben Sulayem.
One described it as "yet another own goal" from the Emirati. Another said: "It could be the beginning of the end for him."
Mercedes, the Wolffs and F1 were not contacted before the FIA announced that it had referred an "allegation of information of a confidential nature being passed to an F1 team principal from a member of FOM personnel" to its compliance unit.
The controversy comes against a backdrop of worsening relations between F1 and the FIA on a number of fronts.
There is unease both inside the FIA and elsewhere in F1 about the way the direction of the governing body under Ben Sulayem.
Ben Sulayem said in February that he was stepping back from direct involvement in f1, a move that came after a series of controversies since he was elected president in December 2021. One of those was the emergence of past misogynistic remarks he had made on an archived website.
But Ben Sulayem has remained active behind the scenes and teams have viewed a series of incidents in recent months as being directly linked to him.
These include the decision to launch a second investigation into Lewis Hamilton crossing the track during the Qatar Grand Prix when he had already been fined and disciplined for it at the race weekend, and the decision to call Wolff and Ferrari team principal Frederic Vasseur to the stewards at the final race of the season for swearing in a news conference.
