The dispute traces back to a 2020 consent agreement between Meta and the FTC.
It resulted in a historic $5 billion fine over privacy breaches.
In May, the FTC accused Meta of non-compliance with the 2020 settlement and proposed substantial alterations to the agreement.
It includes a prohibition on Meta profiting from data collected on minors, extending to information gathered through its virtual reality products.
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Meta's lawsuit was filed in a federal court in Washington, D.C..
It seeks a declaration from the court asserting that certain aspects of the FTC's structure violate the US Constitution.
The company contends that these constitutional violations render the FTC's proceedings against Meta unlawful.
Meta's legal action comes when the Supreme Court's conservative majority shows receptiveness to challenges against the Securities and Exchange Commission (SEC).
The court suggested that individuals accused of fraud by the SEC should be entitled to have their cases decided by a jury in federal court rather than the SEC's in-house administrative law judges.
This echoes some elements of Meta's lawsuit against the FTC.
Senator Edward J. Markey, a frequent critic of Meta and other big tech firms, called Meta's legal move a "weak attempt to avoid accountability."
He said: “In the face of a potentially massive fine, Meta’s adoption of extreme, right-wing legal theories to challenge our country’s premier consumer protection agency reeks of desperation.”