They said the judge had not correctly understood their son's finances.
The judge accused Neymar of only declaring the equivalent of 8% of his assets in 2013.
He said the forward had omitted payments received from advertising and from Barcelona football club.
The judge froze $47.6m (£30.5m) of Neymar's assets.
He said this was to cover potential interest and fines and to prevent the player selling assets before the case was settled.
The judge said the frozen assets were in the name of the Brazilian player and three companies in which he and his parents jointly owned.
However, Neymar's parents said the decision was based on an "incorrect understanding" of their son's income.
"Neymar did not avoid paying taxes, and neither did any of our companies," they said.
Neymar joined Barcelona in June 2013 after a successful career with the Brazilian club, Santos.
But the transfer has prompted fraud investigations in Spain over allegations that the fee paid was much higher than the declared €57m ($65m; £41m).
The parents of the Brazilian football star, Neymar, have denied their son has done anything wrong, after a judge formally accused him of evading $16m in taxes.