"I have instructed my departments to immediately suspend the site www.me.ga," announced Communication Minister Blaise Louembe, saying he wanted to "protect intellectual property rights" and "fight cyber-crime effectively".
"Gabon cannot serve as a platform or screen for committing acts aimed at violating copyrights, nor be used by unscrupulous people," the minister said.
The announcement came after Kim Dotcom unveiled plans last week to re-launch his file-sharing service on January 20, exactly one year after he was arrested in New Zealand on online piracy charges.
The United States accuses Dotcom, a 38-year-old German national who legally changed his name from Kim Schmitz, of fraudulently making more than US$175m on pirated movies, television shows and other content.
The United States wants to extradite him to face charges of money laundering, racketeering, fraud and online copyright theft that could see him jailed for up to 20 years.
Dotcom, who denies the charges, is currently free on bail in New Zealand ahead of an extradition hearing in March.
Louembe said the domain name was to be hosted on Gabon's .ga domain had been allocated to someone in France who transferred it to Dotcom.
The minister said an investigation by his staff had found the site was set up to redirect traffic to another site hosted in France that would provide access to shared files.
The site was still online at 21h00 GMT, with a message saying, "On January 19 this button will change the world."
Dotcom said on Twitter that he was the victim of a US-led "witch hunt" but was not concerned at Gabon's move.
"Don't worry. We have an alternative domain," he tweeted to his 150,000 followers. "This just demonstrates the bad faith witch hunt the US government is on.
Dotcom did not reveal the alternative domain name.
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