The judge ruled that the executives pose a minimum flight risk, authorising their release until a decision is reached on their possible extradition to the US on charges including copyright infringement.
Batato and Van der Kolk were arrested last Thursday along with Megupload co-founder Kim Dotcom and the site's technical officer Mathias Ortmann, after the four were named in an FBI indictment investigation. Dotcom was denied bail earlier this week.
Megaupload, which was shut down by US officials, has been accused of generating in excess of $175 million (£111m) in illegitimate gains, and cheating copyright holders out of more than half a billion dollars.
Judge David McNaughton issued a statement saying that both Batato and Van der Kolk pose a minimum threat of fleeing New Zealand, despite the US government expressing concerns about the latter individual.
"As noted in my earlier decision the possibility of reviving the business from another site outside the jurisdiction of the United States is a factor completely outside the Court's control," he said.
A decision on Ortmann's bail application is expected by the end of the week, reports The Wall Street Journal.
Megaupload and other online storage lockers have numerous legitimate uses, such as sharing files too large to send via email, but US authorities and entertainment bodies believe that their primary use is to facilitate online piracy.
A hearing on the possible extradition of the Megaupload executives may be several months away.