The ruling upheld a decision by the country's parliament in April, but halved the original fine.
However the decision could yet prove fatal with NPD leader, Udo Voigt, admitting in an interview in March that the party was suffering an "existential crisis" due to a lack of funds.
According to the ruling, the far-right party - which receives public funding because of its score in recent elections - must pay the sum that was falsely accounted for.
As the Bundestag has already blocked €300,000 in public funds due to be paid to the NPD, the party must pay out just under a million euros - by May 1.
In May 2008, Berlin's administrative court ordered the party to return nearly €1 million in public funds after uncovering fraud in its accounts from 1997, 1998 and 1999.
A former party treasurer, Erwin Kemma, has been in jail since December 2008 for having embezzled more than €700,000.
The party is not in the Bundestag, but has representatives in two of Germany's powerful regional assemblies.