The comments date back to 2010 before Mursi was elected president and were made during an anti-Zionst conference. However, the New York Times recently obtained a video of those remarks.
The clip showed Mursi saying that "we have to feed our children hate for the Jews and Zionists. We have to be sure not to let them forget".
Mursi, however, said his comment were about the Israeli aggression against Palestinians in Gaza and were "misquoted", a report in Al Masry Al Youm said.
Mursi stressed his commitment to fully respecting Abrahamic religions and freedom of worship, the paper said.
In an attempt to neutralise the damage caused by the remarks, Advisor to Egyptian president for foreign affairs, Essam Al-Haddad, said in a statement that Egypt is committed to freedom of creed, and values religious tolerance. It said the new constitution clearly states so.
However, the statement added that occupation of Palestinian lands has to end for just peace to prevail.
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Mursi was asked about his statements during a meeting with a US congressional delegation led by Senator John McCain.
A statement from the president's office said Mursi also briefed the delegation on his government's efforts to enable all segments of society to build a national consensus on basic principles of democracy, rights and freedoms.
The US government had strongly condemned Mursi's remarks and asked him to repudiate them.
The clip stirred unrest between the Egypt and the US even as McCain was starting his visit to Egypt. McCain also met the Egyptian minister of defence, is meeting representatives of the liberal opposition as well as the Grand Sheikh of Al-Azhar mosque.
Egypt is the second largest recipient of US foreign aid since it signed a peace accord with Israel in 1979. Israel remains the largest.