Users of the file website have been unable to access their data since the site was shut down on January 19, amid allegations of theft of intellectual property and data piracy.
US authorities are now trying to extradite the 38-year-old Megaupload founder Kim Dotcom and three of his colleagues from New Zealand.
A letter filed in the case on Friday by the US Attorney's Office for the Eastern District of Virginia said the data of millions of users could be deleted from the website and third party servers, reported Radio New Zealand.
Prosecutors copied the data needed for their case, and have granted permission for the server's subcontractor's storage companies, Carpathia Hosting and Cogent Communications Group, to start deleting data from February 2.
This move could see the personal photos and home movies of at least 50 million users permanently disappear, as they no longer have access to what they uploaded online because of legal proceedings.
Associated Press business writer Josh Freed broke the story, and told Radio New Zealand this morning there was a chance the personal information of worldwide users, including New Zealanders, could disappear.
"The information that is the focus of prosecutors is allegedly these pirated movies, pirated music, that kind of thing. The company says a lot of families had their own family photos, family movies and personal documents, things that would be perfectly legal.''
Users from around the world can no longer access the site since it was closed, and have been unable to retrieve information online.
He said although the site had an estimated 150 million users, only a third were estimated to be affected by the deletion as there was a variety of spaces to store data on the site.
As the start date of the deletion is scheduled in a few days time, there was still a chance a resolution could be found to prevent personal data being deleted, he said.
"It's possible of course they will work something out ... That leaves a few days here for some kind of court order or some sort of intervention that would put a stop to this.''
