Mr Miller said the move was a "technical legal procedural issue'' which would not have any impact on the charges against Dotcom and his former colleagues.
He said success by Megaupload would also have no impact on the original indictment, which charged Dotcom with criminal copyright
"Even if this particular motion were to be granted ... it would not affect the other defendants in the case, the individual defendants, Kim Dotcom himself or the other corporate entity.''
Mr Miller said he was aware of Dotcom's use of social media to promote his view on the case. He said Dotcom's comments about internet freedom had no merit.
"This case is truly about a criminal enterprise by a career criminal who has been convicted at least three times previously for criminal offences in his life.
"It had one purpose. All of these individuals had one purpose, and that was to generate profits for the people who operated it, including the founder Kim Dotcom who has been convicted of crimes previously in Europe.
"It was a business model founded on using the creative work of others and monetising other people's content.''
Mr Miller also dismissed concerns around the legal obstacles which had emerged in the case. The US has suffered a number of defeats and issues in New Zealand courts with the wrong restraining order used to seize assets and search warrants ruled as too broad.
He said the case was possibly the largest internet piracy case ever heard. "Certainly there will be procedural issues which will be tackled and addressed in a case of this significance and I wouldn't read any more into it than that.''
Dotcom, who is facing extradition to the US, has taken to social media to make known his views over the charges. He launched kim.com last Friday, listing 10 points on the case. He also launched a music video called Mr President, calling for internet users to unite against efforts to control the internet. In five days, it picked up 640,000 YouTube views.