The Romanian Government appears to have backed down on a statement it made last week which suggested there was no Holocaust within the country's borders during World War II.
Israel said the statement ran "counter to historical truth"
A second statement issued on Wednesday said administrations between 1940 and 1945 were "guilty of serious war crimes" and used "methods of discrimination and extermination" against the local Jewish population.
It followed a protest by Israel on Tuesday and a warning that relations between the two countries had been strained.
Correspondents say the remarks also outraged Romania's Jewish community, which normally has good relations with the government.
The new statement recognised the government's responsibility to Holocaust victims.
"By taking over part of the responsibility for the Holocaust victims on behalf of the Romanian state from half a century ago, ... the Romanian Government ... is stressing its wish to continue co-operation with international institutions that are studying the Holocaust problem," it said.
It added that Prime Minister Adrian Nastase and his cabinet had consistently condemned the persecution and killing of Jews and introduced legislation outlawing racist and xenophobic organisations.
Romania's ambassador to Israel was summoned to the Israeli Foreign Ministry on Tuesday to explain the original comments, made on Saturday.
Israel said it "considers with seriousness" the Romanian declaration, which it said ran "counter to historical truth".
According to the Federation of Jewish Communities in Romania, the then dictator of Romania, Marshal Ion Antonescu, was directly responsible for sending 250,000 Jews to their deaths in Nazi concentration camps.
The group says Antonescu was also responsible for inciting a
massacre of between 3,000 and 10,000 Jews in the north-eastern town of Iasi in June 1941.
Antonescu was arrested in August 1944 by then King Michael. He was tried and executed in 1946.