Dotcom's lawyers said they filed an appeal against the decision.
Judge Nevin Dawson's ruling came nearly four years after US authorities shut down Dotcom's file-sharing website Megaupload, which was once one of the Internet's most popular sites.
Prosecutors say it raked in at least USD 175 million, mainly from people using it to illegally download songs, television shows and movies.
The US has charged the men with conspiracy to commit copyright infringement, racketeering and money laundering. If found guilty, they could face decades in jail.
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"It will end up in the Supreme Court, there's no doubt about it," said Dotcom's lawyer Ron Mansfield, referring to New Zealand's highest court. "The legal issues are so interesting and complex."
Judge Dawson, who presided over the nine-week hearing, wrote, "The overwhelming preponderance of evidence... establishes a prima facie case to answer for all respondents on each of the counts."
The judge was required only to decide whether the US had a valid case, and not whether he thought the men were guilty or innocent.
Prosecutors say intercepted communications show the men talking about being "modern-day pirates" and "evil."
Dotcom argued that he can't be held responsible for others who chose to use his site for illegal purposes, and that any case should have been heard in civil court.
The case could have broader implications for Internet copyright rules. Mansfield said that if the US side prevails, websites including YouTube and Facebook would need to more carefully police their content.
The case also raises questions about how far US jurisdiction extends in an age when the Internet has erased many traditional borders. Dotcom says he has never set foot in the US.