Justice Asher said that because Germany did not have an extradition treaty with the United States, Dotcom would be free from prosecution if he chose to escape to his birth country.
"He may or may not have the means to bring about such a scenario, however it was open to the judge and constituted a significant risk which could not be mitigated by [bail] conditions,'' Justice Asher said.
The FBI is seeking to extradite Dotcom and three of his associates to the US to face charges of conspiring to commit racketeering, conspiring to commit money laundering, copyright infringement, and aiding and abetting copyright infringement.
The FBI-led investigation has so far frozen $23 million in a Hong Kong bank account, $10m in New Zealand Government bonds, $6m in expensive cars.
The Megaupload co-founder showed signs of a sore back as he sat through the nine-hour court hearing and had to have his seat changed.
Dotcom, also known as Kim Schmitz, addressed the court for the first time since being arrested last month and said he had every intention of fighting the charges so that he could get back the millions of dollars frozen by the FBI.
"I'm aware that if I go to Germany I would be unable to unfreeze my assets. What I want to do is stay here to fight and get my money back. What would I do in Germany with five kids and a wife with no money?
"It is not an option for me.''
Crown prosecutor Anne Toohey, acting for the US Government, said there could be more money. She also said the court had to take into account the issue of flight risk, given Dotcom was found to have travel documents and credit cards in different names.
She said New Zealand had porous boarders and Dotcom had access to a helicopter.
Dotcom's lawyer Paul Davison QC said his client had changed his name for legitimate reasons and had no intention of deceiving officials.
He said that explained the passports and credit cards in different names.
"You left with a business man reeling from the fact that his business has been brought to a halt, his assets have been seized, his family is effectively devastated by this event.''
Earlier, Dotcom told the court how, while on remand, he had received letters from female prisoners and even a phone call from a man claiming to be a "prosecutor'' and asking for money in exchange for a favourable bail appeal.
Dotcom said he reported the phone call to prison authorities.
Fresh from visiting Dotcom in the cells after Justice Asher's decision this evening, Mr Davison told media outside court his client was disappointed with the decision.
Mr Davision described suggestions that Dotcom could flee the country by boat or jet as a "flight of fancy''.
He said Dotcom would now take advice on his next steps which could include a further appeal or a fresh application if his circumstances change.
Extradition papers against Dotcom are expected to be filed later this month.
Dotcom and his millions:
* $30 million rented mansion in Coatesville
* $10 million invested in NZ government bonds frozen
* Over $100 million assets frozen worldwide
* $42 million earned in 2010 year alone, according to the FBI
* $6 million worth of luxury cars removed from the property
Dotcom case at a glance:
January 18: District Court issues arrest warrant for Dotcom and three others
January 20: Police raid Dotcom's Coatesville mansion. Dotcom and three associates arrested
January 23: Dotcom applies for bail at the North Shore District Court
January 25: Judge McNaughton declines bail at the North Shore District Court
February 03: Dotcom's bail appeal at the High Court in Auckland declined by Justice Asher
