Israel has summoned the Vatican's ambassador to explain why the Pope left the country off a list of those recently hit by terrorism.
Pope Benedict has yet to address the Israeli-Palestinian conflict
Pope Benedict XVI on Sunday deplored attacks in "countries including Egypt, Turkey, Iraq and Britain".
Israel said he had failed to mention a 12 July suicide bombing in Netanya that killed five Israelis.
The foreign ministry said it would be interpreted as "granting legitimacy to... terrorist attacks against Jews".
"We expected that the new Pope, who on taking office emphasised the importance he places on relations between the Church and the Jewish people, would behave differently," the ministry said in a statement.
The Vatican embassy declined to comment.
Pope Benedict has accepted an invitation to visit Israel but has yet to comment on the Israeli-Palestinian conflict in public since taking office in April.