Michaloliakos and five of his party lawmakers were among 20 people arrested over the weekend in a crackdown against the Nazi-inspired party following the Sept. 17 fatal stabbing of rap singer Pavlos Fyssas. A man arrested at the scene of the attack identified himself as being involved in Golden Dawn.
The court also ordered Giorgos Patelis, the head of Golden Dawn's local office in the area west of Athens where Fyssas was stabbed, to be remanded in custody.
A sixth party lawmaker, Christos Pappas, who the prosecution has described as Michaloliakos' second in command, is to appear in court for his preliminary hearing later Thursday morning.
The party has vehemently denied any role in the killing.
It is the first time since democracy was restored in Greece in 1974 after a military dictatorship that sitting members of parliament have been arrested and jailed.
The government, which has vowed to eradicate the group, has argued the party has been acting as a criminal organization rather than a political party.
Golden Dawn, which the government has described as a "Nazi creation," rose from the margins of Greece's political scene to become the third most popular party in Greece amid the country's severe financial crisis. It won nearly 7 percent of the vote and 18 of Parliament's 300 seats in 2012 general elections.
It has long been blamed for a series of violent attacks, mostly against immigrants. The party denies it is behind any violence.
Rights groups and medical charities have long warned of an increase in the viciousness and frequency of attacks attributed to Golden Dawn members or supporters. Two men arrested in January for the fatal stabbing of a Pakistani migrant were believed to be supporters of the group. But Fyssas' death was the most serious crime attributed directly to an alleged party member.
On Wednesday, party lawmaker Yiannis Lagos was also jailed pending trial. Golden Dawn spokesman Ilias Kasidiaris, also a lawmaker, was released on a 50,000 euro ($67,770) bail, while no bail was set for the other two lawmakers who were released, Ilias Panagiotaros and Nikos Michos. All three were banned from leaving the country.
They stormed out of the court building, with Kasidiaris punching a television cameraman and kicking a photographer as he went. They swore at and threatened journalists as they headed out of the court complex, and later as they left police headquarters after collecting their personal belongings.
The party has argued that the case against them is politically motivated.
The government insisted the case against the Nazi-inspired party was still on track despite Wednesday's releases.
"This essentially changes nothing. Their charges stand, the investigation is ongoing and the evidence is being gathered," said Interior Minister Yiannis Michelakis. "We are at the first stage of this investigation."
A total of 32 arrest warrants were issued in the case, including two for police officers. Authorities have been continuing raids on the homes of police officers with suspected ties to criminal activities allegedly linked to the party.