A top aide to Greek PM Antonis Samaras has resigned over a videotape in which he appears to accuse his boss of influencing a criminal investigation.
In the video, Panayiotis Baltakos is seen speaking to a spokesman for the far-right Golden Dawn party about the arrest of its leaders in September.
Golden Dawn accuses the conservative-led coalition government of persecuting it for political reasons.
A government minister rejected the accusation as a fantasy.
The latest developments are at the very least an embarrassment for the government but will also be seen as further evidence that Greece's judiciary is not independent and that the case against Golden Dawn is on shaky ground, the BBC's Mark Lowen reports from Athens.
Since coming to power at the head of a broad coalition government in June 2012, Mr Samaras has been credited with putting the debt-ridden eurozone country on the track to economic recovery.
It is now forecast to exit six years of recession this year, its deficit has been wiped out - save for interest on the bailout - and Athens is preparing a return to the markets for the first time since 2010.
At the last general election, in June 2012, Golden Dawn won 7% of the vote to 30% for Mr Samaras's New Democracy party.
Golden Dawn's spokesman, Ilias Kasidiaris, was among seven party MPs arrested in September, charged with being part of a criminal group.
Mr Kasidiaris, who was subsequently released, was in parliament on Wednesday to challenge a move to lift immunity from prosecution for himself and a further four other Golden Dawn MPs.
In the event, all five MPs were stripped of their immunity. They may now be arrested or questioned on suspicion of being part of a criminal group.
Arguing his case that Golden Dawn was being victimised for political reasons, Mr Kasidiaris released the tape of his conversation with Mr Baltakos.
In the recording, Mr Baltakos can be heard saying that Golden Dawn's leaders were put in jail at the request of government ministers.
Mr Baltakos can also be heard saying that the authorities did not have evidence against Golden Dawn.
Announcing his resignation, Mr Baltakos issued an apology in which he said that his comments had only been intended to appease Golden Dawn officials who had accused him of conspiring against them.
Public Order Minister Nikos Dendias, who also figures in the conversation on the tape, said the accusations against the government were "figments of the sick imagination" of Mr Baltakos.
Justice Minister Haralambos Athanassiou also denied any effort to influence the investigation.
The crackdown on Golden Dawn in September followed the murder of a leftist rapper, Pavlos Fyssas, allegedly by a Golden Dawn member. Two members of the party were killed and a third wounded in a drive-by shooting outside the party's offices in an Athens suburb in November.
If the case against Golden Dawn's leaders were to collapse, the backlash against the government would be substantial and Golden Dawn's support would almost certainly soar yet further, our correspondent says.