The US government claims that co-founder Kim Dotcom and his associates committed fraud against the streaming service in 2006, adding the charge to a list of allegations that includes piracy and racketeering.
In its January 5 indictment against the company, America's Justice Department included an excerpt from what it claims is an email conversation from the period in question between Megaupload executives Mathias Ortmann and Bram van der Kolk.
"Do we have a server available to continue downloading of the Youtube's vids?" van der Kolk allegedly wrote to Ortmann. "Kim just mentioned again that this has really priority."
"Hope YouTube is not implementing a fraud detection system now... praying," Ortmann is said to have responded. "Well we only have 30% of their videos yet. In my opinion it's nice to have everything so we can decide and brainstorm later how we're going to benefit from it."
US authorities shut down Megaupload earlier this month, and charged seven men, including Dotcom, van der Kolk and Ortmann, with copyright infringement, racketeering and money laundering.
Dotcom, van der Kolk and Ortmann - who are all New Zealand-based - are currently awaiting a decision on their possible extradition to the US. Van der Kolk was released on bail last week, along with fellow Megaupload manager Finn Batato. Dotcom's bail was denied, while Ortmann's is pending.
The Megaupload indictment also accuses the company of participating in a smear campaign against its rivals, alleging that they took part in the very practises Dotcom and his business partners have been charged with.
"Our legal team in the US is currently preparing to sue some of our competitors and expose their criminal activity," DotCom allegedly wrote to a PayPal representative in October 2011. "We'd like to give you a heads up and advise you not to work with sites that are known to pay uploaders for pirated content.
"They are damaging the image and the existence of the file hosting industry (see what's happening with the ProtectIP act). Look at Fileserve.com, Videobb.com, Filesonic.com, Wupload.com,Uploadstation.com.
"These sites pay everyone (no matter if the files are pirated or not) and have NO repeat infringer policy. And they are using Paypal to pay infringers."
Megaupload's attorney Ira Rothken maintains his clients' innocence, calling the charges against them "flimsy".