Several other sources said Khelaifi and a close associate were questioned by investigators in March "as a person of interest" in the investigation.
Qatar was unsuccessful in its bid to host the championships, which went to London. But Qatar did go on to secure the rights to hold the 2019 world championships to be held in October.
The move by an investigative judge is a demonstration of the broadening scope of France's inquiry into a suspected web of corruption once rife in world athletics, including bribes to cover up athletes' positive drug tests.
"The judge has made a mistake. Nasser has no involvement at all," Khelaifi lawyer Renaud Semerdjian told Reuters. "His name does not appear in the entire procedural file."
Semerdjian also questioned the competence of French prosecutors to delve into matters he said took place outside of France.
Khelaifi, 45, is deeply involved with sports and sporting events in Qatar. He serves as chairman of Qatar Sports Investments and the Qatar Tennis Federation, alongside his role as president of Paris Saint-Germain. He is also a minister without portfolio in the Qatari government.
The judge's decision means Khelaifi is now formally treated as a suspect and takes the legal process one step closer to trial. Under French law, however, a suspect is not formally charged with a crime unless he is sent to trial.
French prosecutors this week recommended that Lamine Diack, the Senegalese former head of the IAAF, and his son stand trial for a host of suspected illicit practices, committed over a number of years with the active involvement of athletes and their federations.
They began their investigation into Diack in 2015, shortly after the IAAF's ethics commission and the World Anti-Doping Authority (WADA) uncovered evidence that a Russian athlete paid a six-figure sum to cover up a positive test.
In the four years since, the French inquiry has widened to include the bidding process for the Rio de Janeiro and Tokyo Olympic Games, as well as the world athletics championships.
The investigative judges presiding over the Diack case accuse the Senegalese of favouring Qatar's bid for the 2017 world championship in return for a kickback, sources have said.
The indictment handed to judges on Monday and seen by Reuters accuses Diack and his son, Papa Massata, of bribe-taking and money laundering.
France's financial prosecutors allege that Pamodzi Sports Consulting, a company belonging to Papa Massata, received $3.5 million from Oryx QSI, just one of several multi-million dollar payments received by the Diacks.
A source familiar with the matter said Oryx QSI had undertaken to pay $32.5 million for the commercial rights to the 2017 championships of which $3.5 million was paid upfront as a non-refundable deposit. The full amount was conditional on Qatar winning the bid, the source said.
London won the bid in November, 2011, to host the 2017 world championships.
Khelaifi's lawyers said he was the chairman of Qatar Sports Investments but in 2011 had nothing to do with Oryx QSI, which they said was a separate entity.
"Nasser al Khelaifi was neither a shareholder nor a director of Oryx in 2011. He was not directly or indirectly involved in Doha's bid to host the 2017 world athletics championships," Khelaifi's lawyers said.
Oryx QSI could not immediately be reached for comment.
Nasser Khelaifi is also chairman of beIN Media Group, a television network that holds regional rights to many of the world's top sporting events, including World Cup soccer.
He is currently under investigation in a separate case by Swiss prosecutors for providing "undue advantages" to soccer's global governing body FIFA for broadcasting rights for the 2026 and 2030 World cup.
The IAAF told Reuters on Wednesday it had in 2016 introduced "wide ranging reforms right across the sport, including its decision-making and approval processes, overall governance at every level of the sport".
(Reporting by Emmanuel Jarry and Eric Knecht Writing by Richard Lough Editing by Luke Baker and Mark Heinrich) ((Email: email@example.com; Tel: +33 1 49 49 52 42; Reuters Messaging: firstname.lastname@example.org))