Those claims were made in a dossier compiled by Mr Dotcom's lawyers and released wile Mr Holder, the fourth-ranked member of President Obama's cabinet, was in Auckland to attend a meeting of his counterparts from the United Kingdom, Australia, and Canada, hosted by New Zealand's attorney general Chris Finlayson, QC.
"Again I don't want to comment specifically on the case other than to say that all of the actions that we have taken in connection with this and other matters have been consistent with our priorities to deal with the theft of intellectual property and so this case has not been treated in any way different than any of the others that we have brought. All of these matters, this case as well, are based on facts and based on the law and nothing more than that."
Mr Holder confirmed he had discussed the case with Mr Finlayson when the pair met this week and said he was satisfied with the cooperation the US had got from New Zealand authorities.
In cooperating with the FBI, Mr Dotcom, a New Zealand citizen, was spied on illegally by New Zealand's Government Communications Security Bureau and his mansion raided using an unlawful search warrant.
The Government is seeking a law change to allow the agency to spy on New Zealand citizens in certain circumstances.
Read more: Live chat replay: Kim Dotcom