As the strange case of file-sharing site Megaupload continues to unfold, many wonder if the federal government will begin to clamp down on similar sites that function like Megaupload, with easy sharing and hosting of copyrighted files.

Already, two well-known file-sharing services, Uploaded.to and Filesonic have disabled several features of their sites this weekend because of the Megaupload scandal. Others are sure to follow.

But Derek Labian, CEO of popular cloud-based file-hosting site MediaFire, told VentureBeat in an interview today that he isn’t too concerned about the government going after his company because, unlike Megaupload, MediaFire doesn’t incentivize piracy.

“We don’t have a business built on copyright infringement.” Labain said. “Like many other cloud-based sharing services like Box.net and Dropbox, we’re a legitimate business targeting professionals.”

When it comes to Megaupload, Labian described Kim Dotcom and his organization as “shady” and said the $175 million in revenues the company made should give people pause. He noted that Megaupload’s structure gave users monetary rewards for uploading pirated content. Users of the service could upload without a cap but users who want to download a large file (or download it faster) would have to pay for it. Those who uploaded the best files would be given free account upgrades or even cash.

“Megaupload was making a ridiculous amount of money with a ridiculously bad service,” Labian said. “We frankly don’t see ourselves in the same space.”

A little more background on MediaFire: The privately funded company out of Woodlands, Tex. was founded in 2006 and has steadily offered better ways to host and share large files. Because it offers an incredibly easy to way to share 200MB files for free with other people, the company has attracted employees at 86 percent of the Fortune 500 for sending files that are too large for e-mail. It offers unlimited downloads and file storage, and if you want to upload larger files with long-term storage, you can pay $9 a month for a Pro account or $49 a month for a Business account.

But the company’s free file-sharing solution can also be used easily for sharing copyrighted files, especially music, with friends, relatives or anyone on the web. A Google search for a song name, an artist name and “MediaFire,” for example, will likely bring you to a copy of that file that can easily be downloaded from a MediaFire page.

When asked about the Googling issue, Labian said that MediaFire is a “private service” and the only reason Google indexes a MediaFire page is when it has been shared by a user on a third-party site. He said MediaFire isn’t at fault for this and said Google should look into the issue.

“We try to steer clear of things that would attract scrutiny,” Labian said. “If people are pirating on our service, we don’t want those people to use it.”

Another reason Labian said he wasn’t worried about the government stepping in is because the company maintains a “good relationship” with various government bodies, including “Homeland Security, ICE, and the FBI.” Following DMCA protocols, whenever MediaFire is notified of a copyrighted file being shared inappropriately, the company immediately takes it down.

As for the future, MediaFire is optimistic about what’s to come. Labian said the company has been working for a year on its next set of products, which will emphasize collaboration and focus on business users. He teased what was coming by saying that cloud storage providers Box.net and Dropbox significantly disrupted the cloud storage space, but MediaFire would do it next.

“This is a tough market to be in, but we’re constantly looking to innovate,” Labian said. “Sharing will always be important, but it’s not the only important aspect for our customers.”