The libertarian leader and his office denied involvement with creators of the $LIBRA cryptocurrency, saying he initially drew attention to it Friday as an entrepreneurial project that might benefit Argentina but learned more about it later and then withdrew his support.
Lawyers in Argentina filed fraud complaints against the libertarian President on Sunday.
The case was assigned on Monday to federal Judge María Servini in Buenos Aires.
She does not have a deadline to finish investigating the allegations.
In a tweet on Friday that coincided with the launch of the $LIBRA crypto coin, Milei said it was aimed at "encouraging economic growth by funding small businesses and start-ups".
It enjoyed a brief spike in value above $US4 billion ($6.3 billion) in market capitalisation, although its value began to decline amid comments of critics that it could be a scam.
Milei deleted the post a few hours later as the value of the cryptocurrency was collapsing in a downturn that caused millions of dollars in losses to many of its new investors.
The coin, developed by KIP Protocol and Hayden Davis, could be obtained by accessing a link that directed users to a website called vivalalibertadproject.com, referring to the phrase "Viva la libertad!" that Milei uses to close speeches and messages on his social media.
The president's office said Milei was not involved in any stage of the cryptocurrency's development and decided to remove his post to avoid speculation and limit further exposure, following the public reaction to the project's launch.
"The president shared a post on his personal accounts announcing the launch of KIP Protocol's project, as he does daily with many entrepreneurs who wish to launch projects in Argentina to create jobs and attract investments," the president's office said.
After deleting the post, Milei said on X he was unaware of the details of the cryptocurrency, and accused his political opponents of trying to exploit the episode.
"I was not aware of the details of the project, and after getting informed, I decided not to continue promoting it (which is why I deleted the tweet)," he said.
His office also said the country's Anti-Corruption Office would investigate the case.
Jonatan Baldiviezo, a lawyer and one of the plaintiffs, alleged Milei's actions were part of an illicit association to commit "an indeterminate number of frauds" in the episode.
"Within this illicit association, the crime of fraud was committed, in which the president's actions were essential," he said.
