Dotcom's alleged co-offenders, Bram van der Kolk, 29, Finn Batato, 38, and Mathias Ortmann, 40, had their hearings adjourned until tomorrow.
"My decision on Mr Dotcom will probably determine which way it goes for their applications," said Judge McNaughton. "It's still an open question in my mind - I still haven't resolved the issue."
Dotcom, wearing the same clothes he appeared in on Friday, sat next to his lawyer, Paul Davison, QC, throughout the hearing. There was standing room only as his supporters crammed into the public gallery.
"First and foremost, I want to say that Mr Dotcom emphatically denies any criminal misconduct or wrongdoing such as alleged in the indictment," Mr Davison said. "He denies the existence of any mega conspiracy ... or that he was involved in any criminal enterprise relating to infringing copyrighted works."
He said Dotcom had planned to go to Hong Kong yesterday with his wife, Mona, who is due to give birth in April. She wanted to have the babies in Hong Kong with a doctor she trusted. He said that plan was ruined when police "assaulted" Dotcom Mansion on Friday.
Mr Davison claimed police landed helicopters "dangerously" at the property in an "unprecedented" manner, aiming to cause shock and anxiety to those home at the time. "It was unneccessarily aggressive."
Dotcom was in bed, and after hearing the helicopters land, which was not an unusual event at the mansion, he believed there was a "security risk" and followed the mansion's safety plan - he went into the panic room, where he was found by police sitting cross-legged on the floor. "He was anxious and frightened and wasn't sure what was going on. He heard people shouting 'police' and remained where he was. He was so frightened that he'd just stayed there."
Mr Davison claimed a police officer visited the mansion the day before and took secret footage of the property to aid the planning of the raid. He said the head of security at the mansion told the officer that Dotcom's wife was heavily pregnant, and that with that knowledge police acted irresponsibly in the way they approached the property, posing significant risk to the woman and her unborn children.
The Crown, acting on behalf of the US Government, opposed bail, saying Dotcom was an "extreme" flight risk and there was a significant chance he would reoffend while on bail by re-establishing the website.
Crown lawyer Anne Toohey said Dotcom had access to multiple passports, and in the past had used his fortune to charter private helicopters, jets, and yachts. That meant there was a danger he would try to flee the country. "He appears to have a pilot available to him whenever he needs one. Mr Dotcom presents extreme risks."
Mr Davison argued his client was not a flight risk because all his accounts had been frozen, bar one at Rabobank with a balance of about $300,000. He held four passports, two of which were seized by police from beside a bed. They also seized three wallets with 16, 19 and 10 credit cards in each. Mr Davison said most of the cards were out of date.
"So while there were quite a lot, he was a collector of them. The passports were beside a bed that he uses as a work location. This is a man who will be residing here with his wife, children, and two guardians of his wife. He is not a person who is inherently motivated to disappear or breach conditions. There is no flight risk."
He said Dotcom had no way of re-establishing Megaupload, so the risk of reoffending was nil. "The business has been shut down ... there is no ability to start this business up on a computer anywhere. Mr Dotcom can assure the court that he has no intention of re-establishing the business. If there is an ability to do anything of that nature, he is not going to do it until the legalities of the issue are resolved."
