Israeli Prime Minister Ariel Sharon has moved to end a dispute with the Vatican by writing a letter to the Pope.
Pope Benedict XVI has accepted an offer to visit Israel
Israel's envoy to the Vatican said he hoped the letter - which described the Pope as "a true friend of Israel" - would lead to better relations.
The row erupted when Israel complained that Pope Benedict XVI had left Israel off a list of countries recently hit by terrorist attacks.
The Vatican then accused Israel of trying to "distort" the Pope's words.
Ambassador Oded Ben Hur said he had handed over the letter this week in an "amiable and intimate" meeting with Vatican officials.
"This disagreement is now behind us," said a spokeswoman for Israel's embassy to the Holy See.
"This letter allows us to put an end to the story, making the necessary clarifications."
The Pope is due to meet Israel's two chief rabbis in mid-September.
Italy's Corriere della Sera newspaper quoted the Vatican ambassador to Israel, Pietro Sambi, as saying: "I'm pleased that this has ended well. The clarifications were satisfactory."
The newspaper cited Israeli sources as saying they admitted their government had been "too aggressive" in reacting to the Vatican's omission of Israel from a list of countries affected by terrorism.
But Ambassador Ben Hur denied the newspaper's claims.
Vatican Secretary of State Cardinal Angelo Sodano is meanwhile reported to have said that while the omission was accidental, the Vatican could have been more sensitive.
On 24 July, in a Sunday address watched by millions, the Pope condemned recent terrorist bombings in Egypt, Turkey, Iraq and Britain.
He did not mention a Palestinian suicide bombing the previous week, prompting angry protests from Israel that the omission "strengthens extremists opposed to peace."
The Vatican dismissed the complaint, saying it could not condemn every Palestinian strike, and also saying that some Israeli attacks were worthy of condemnation.
Pope Benedict has accepted an invitation to visit Israel, but no date has been set.