Miron Cristea is one of five Romanian Orthodox Church patriarchs the bank has honoured with a silver-minted coin.
But after a complaint from the US Holocaust Memorial Museum, the bank's governor has agreed to review the coin.
"We did not wish to send a racist, xenophobic or anti-Semitic message," said Mugur Isarescu.
"We respect the values of the nation and democracy," he added.
'Demonised Jews'Mr Cristea led Romania's Orthodox Church between 1925 and 1939, and was the country's prime minister from 1938-39.
As prime minister, he amended the citizenship law, thereby stripping 225,000 Jews (37% of the country's Jewish population) of their Romanian citizenship.
In a study published in 2004, an international commission of historians said that Mr Cristea had "demonised the Jews" and had called for their deportation.
Some 300,000 Jews and gypsies were killed in Romania during the Holocaust.
After the new coin was minted, the National Bank of Romania received a letter of protest from a director at the United States Holocaust Memorial Museum, in Washington DC.
Radu Ioanid, who runs the museum's international archives, said he was "shocked" by the coin and called for it to be withdrawn.
The coin also sparked protest from Romania's Jewish community.
"I can't understand how the patriarch managed to pass through the filter. It is known there are black stains connected to his attitude towards the Jews," said Robert Schwartz, representative for Romanian Jews in the city of Cluj.
Mr Isarescu rejected accusations of racism, saying the bank was making "a clear distinction between the patriarch and the prime minister".
But he said the bank had agreed to set up a commission that would "analyse the situation and come up with a solution".
Mr Isarescu said the coin may be scrapped if it was considered to be anti-Semitic, which is illegal in Romania.
"The decision should be made public in a few days' time," he said.
SIC: BBC