Nikos Michaloliakos was one of six MPs arrested over the weekend amid outrage over the recent murder of an anti-racist musician.
Three of the detained MPs have been freed pending trial while a fourth was remanded in custody.
All four denied the charges against them during a marathon court hearing in Athens.
In all, 22 people were detained following the September 18 murder of Pavlos Fyssas.
A man held for the stabbing told police he was a Golden Dawn supporter, though the party strongly denies any link.
Nikos Michaloliakos faces charges including murder, assault and money-laundering.
According to Greek law, he will set out a preliminary defense argument when he appears before an investigative judge on Wednesday.
The judge will then decide – on the basis of the charges and the defense statement – whether to grant bail or remand Nikos Michaloliakos in custody pending his full trial, which the authorities are keen to conclude swiftly.
MP and party spokesman Ilias Kasidiaris was freed on Wednesday on bail of 50,000 euros ($68,000) and banned from leaving the country. Fellow MPs Ilias Panagiotaros and Nikos Michos were freed under travel bans but with no bail set.
A fourth MP, Yannis Lagos, was remanded in custody.
The plea session lasted 18 hours, Reuters news agency reports.
Nikos Michaloliakos’s deputy, Christos Pappas, is set to appear in court in the coming days.
Any MPs finally convicted would lose their seats in parliament, prompting by-elections and – the government hopes – leading to the destruction of Greece’s neo-Nazi party.
During Tuesday’s court appearances, there was a heavy presence of riot police – a reminder that despite falling popularity in the opinion polls, the party still commands significant support.
Supporters outside court chanted slogans, including “You are heroes!”
Details from witness testimony have been emerging about the way in which the party operated.
The testimony speaks of a strict hierarchical structure – or “Fuehrer principle” as the indictment calls it – as well as assault squads and military-style training.
Searches of the homes of some MPs have found Nazi paraphernalia as well as unlicensed weapons, ammunition and bundles of cash.
The crackdown was sparked by outrage at the murder of rapper Pavlos Fyssas, 34, whose stage name was Killah P.
George Roupakias, 45, who said he was a supporter of Golden Dawn, was arrested in connection with the killing.
On Friday, Golden Dawn – which won nearly 7% of the vote in 2012 elections – threatened to pull its 18 MPs out of the 300-strong parliament.
The governing coalition headed by PM Antonis Samaras, which has 155 seats, would then face by-elections.
Speaking on a visit to the US on Monday, Antonis Samaras vowed to eradicate the “shame of neo-Nazism”.
In recent months, Golden Dawn has been accused of perpetrating attacks on migrants and political opponents.
Golden Dawn officially denies being a neo-Nazi movement, despite its swastika-like insignia.
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