The scandal, known as "uranium-gate", resulted from a 2011 transaction between French nuclear giant Areva and companies both in Niger and abroad.
There is also a French investigation into some of Areva's business dealings, with aspects related to this deal.
Areva has not commented on the legal case in Niger, but says it is cooperating in the French enquiry.
Niger is one of the biggest uranium producers in the world and the metal is the country's largest export.
Many people turned up on Friday morning outside the court in the capital, Niamey, as representatives of civil society movements arrived to register the court action, the BBC's Himadou Hamadou said.
Their complaint alleges embezzlement of public funds, money laundering, forgery and conspiracy to defraud.
The legal action centres on the allegation that Areva in 2011 bought a stock of uranium from Niger at a discounted price.
Niger has two significant uranium mines that provides 7.5% of the world mining output from Africa's highest-grade uranium ores, according to the World Nuclear Association, the international organisation that represents the global nuclear industry.
Niger's first commercial uranium mine began operating in 1971, with a strong government support for expanding uranium mining.

The Legend of Barney Thomson will open the 69th year of the festival on Wednesday 17 June.
The film, which stars Carlyle alongside Emma Thompson and Ray Winstone, will receive its world premiere at the start of the 12-day festival.
Mark Adams, the new artistic director of EIFF, said he was "thrilled".
Tickets for the film's public screening at Edinburgh's Festival Theatre go on sale on Wednesday.
Starring alongside Carlyle, Thompson and Winstone are Tom Courtenay, Ashley Jensen, Martin Compston, Brian Pettifer, Kevin Guthrie, James Cosmo, Stephen McCole and Samuel Robertson, with a screenplay by Colin McLaren and Richard Cowan.
Mr Carlyle said: "After a career-long association with EIFF it gives me enormous pleasure to have The Legend of Barney Thomson chosen as opening night film.
"It really is such an honour for me to have my first feature as director premiered here in Edinburgh at the festival that has played such a huge part in my life."
Mr Adams said: "We are thrilled to be opening this year's festival with Robert Carlyle's wonderful black comedy.
"It is a marvellously macabre and playful film, impressively directed and with a terrific cast.
"It is the perfect film to kick off what promises to be an exciting festival."
Based on the book "The Long Midnight of Barney Thomson" by Douglas Lindsay, the film is a dark comedy that tells the story of Barney (Carlyle), an awkward barber who inadvertently stumbles into serial murder.
Activists in Niger have started legal action into a uranium deal in which the country is said to have lost $3.25m.
[NEXT_CONCEPT]
Movie star Robert Carlyle's directorial debut film is to open the Edinburgh International Film Festival, it has been announced.