Panagiotis Baltakos, general secretary of Samaras's cabinet, was filmed apparently having a discussion with Golden Dawn spokesman Ilias Kassidiaris, one of the many senior party cadres facing criminal charges.
A voice resembling that of Kassidiaris can be heard on the video posted on Greek news sites and seen by AFP.
Baltakos is shown saying that the Supreme Court prosecutor who finalised criminal charges against the group had been "persuaded" to do so by Justice Order Minister Haralambos Athanassiou and Citizen's Protection Minister Nikos Dendias.
The Greek media said Kasidiaris released the video amid efforts by Golden Dawn to show that the judicial probe that has already placed one-third of the group's lawmakers in pre-trial detention is politically motivated.
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"I told him Golden Dawn will go to 20 per cent, he called me a wanker," he says in the discussion.
"There is no reality in talk of a 'plot'," Baltakos said.
The blow for the government came as the tide had appeared to turn for the neo-Nazi party, which had massively boosted its strength in the past two years.