Dotcom's lawyer Paul Davison QC told the court the warrants were unlawful and the whole process had been "woefully, ineptly handled".
He said warrants should give sufficient detail before an intrusion into a person's private life was authorised by law. But the seizure of items from Dotcom's mansion was "wholesale and indiscriminate" and an unprecedented invasion of privacy, he said.
Police had acted on the authority of the Attorney-General, after receiving a request from US authorities, in executing warrants to seize items relevant to alleged breaches of copyright and money laundering.
Those allegations were categorically denied by Dotcom.
Police had seized a vast number of items, including personal computers and hard drives belonging to Dotcom and his family, Mr Davison said.
Some 150 terabytes of data was seized, which was equivalent to 150 million books of 500 pages each. That illustrated how expansive and indiscriminate the seizure was, he said.
Clones of hard drives had been handed to US authorities but Dotcom was still being denied access to his own data, which Mr Davison said was a "gross miscarriage of justice" arising from the unlawful warrants.
Earlier, Mr Boldt said the Crown did not shrink from the fact there were errors in the warrants, but those errors did not make the warrants invalid.
"It simply is a case of clumsiness or sloppiness in translating the application into a warrant."
The warrants were not excessively broad, and set out to do exactly what Justice Winkelmann said they ought to, he said.
The warrants had not specified that they pertained to electronic copyright infringement, but only that they pertained to copyright infringement.
However, when looking at the items and the context in which they were seized, there were some "pretty good clues" as to what the warrants related to, Mr Boldt said.
It was clear from the warrant applications that Dotcom's Megaupload business was a "front" that purported to act as a legitimate file storage and file sharing site, he said.
The warrants made it clear the entire business was a copyright infringing entity designed to look like a legitimate entity, and therefore anything that contained evidence about the business would be relevant to the criminal inquiry.
On the issue of the hard drive clones, Mr Boldt said there was a legal difference between seized items and the information contained on them.
He agreed the clones had not been handed over with any conditions on what US authorities did with them. But he said that was a matter for the Attorney-General's discretion, not for the District Court judge who issued the warrants.
Mr Davison's submissions were also adopted by Dotcom's three co-accused - Finn Batato, Mathias Ortmann and Bram van der Kolk - who were arrested on the same day as the Dotcom mansion raid in January last year.
None of the men were present for today's appeal hearing.
Justices Ellen France, Anthony Randerson and Douglas White reserved their decision.
