Asked by public radio RTE whether it might be better to yield to political pressure and wind down the bank as quickly as possible, Cowen said:
"The idea that it could be wound up with us having to come up with upfront costs of winding up that bank to the tune of 70 or further billions clearly wouldn't be in the interests of the taxpayer."
Anglo's new management has proposed carving out a small functioning bank via a "good bank/bad bank" split but government ministers have signalled a shift in policy towards an eventual wind-down.
A wind-down over 10 or 20 years -- among scenarios under examination -- could still entail substantial additional costs beyond the 25 billion euros so far earmarked for the lender and could trigger a further rise in Ireland's borrowing costs.
Cowen already said in early June that an immediate liquidation of the bank would mean a fire sale of assets and capital losses of at least 40 billion euros to the state.
He also said in June that the government would have to provide 70 billion euros of cash to meet deposits, bondholders and liabilities to the European Central Bank in an immediate windup.
However, political and market pressures have increased since then.
With investors looking for certainty on the bank's fate, Cowen said the government was at an advanced stage in discussions with the European Commission and final documentation had already been sent to Brussels on the matter.
"We're anxious to bring it to finality as soon as our discussion with the European Union are completed," Cowen added.
(Reporting by Andras Gergely and Padraic Halpin; editing by Patrick Graham)
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