Finance Minister Michael Spindelegger (ÖVP) had said that the taxpayer would pay €5.3 billion in 2014 to the ÖBB.
However, the finance ministry has now told national broadcaster ORF that subsidies were counted twice - which led to a miscalculation of €600 million.
The ÖVP had declared that it wanted to save €1 billion within the ÖBB in 2014. It is not yet clear to which extent this amount was to be revised with the new figures.
Minister of Infrastructure Doris Bures (SPÖ) rejected the ÖVP's plans on Tuesday, saying that either they had "no knowledge of the subject" or were "acting maliciously".
ÖBB chief Christian Kern said on Monday that he could not understand why a ruling party like the ÖVP spoke in such a negative manner about the ÖBB.
Kern also criticised Spindelegger's idea to sell the ÖBB's power plants, saying then the state railways would have to pay a higher price for electricity.