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The Gabon government said it was immediately suspending the me.ga site to "protect intellectual property rights" and "fight cyber crime effectively", the phys.org website reported.
The country's Communication Minister Blaise Louembe said Gabon could not "serve as a platform or screen for committing acts aimed at violating copyrights, nor be used by unscrupulous people".
Me.ga is the follow-up to Megaupload, which was shut down in January when police swooped on the Dotcoms' Coatesville mansion outside Auckland to seize computers and other evidence.
It was due to be hosted on Gabon's .ga domain.
Dotcom, a German national who holds New Zealand residency, faces an extradition hearing in March even though a New Zealand court ruled that the January raid and seizure were unlawful, and the nation's spy agency was found to have illegally spied on Dotcom.
On Twitter, Dotcom said he had an alternative domain.
"This just demonstrates the bad faith witch hunt the US government is on."