The pontiff also said in separate comments Monday that he didn't see any anti-Christian motive in recent attacks blamed on Muslim extremists and urged dialogue with the best elements of Islam.
The German-born Benedict, who has consistently reached out to Jews since assuming the papacy, was criticized by Israel for remarks Sunday from his Alpine vacation retreat in northwestern Italy.
He prayed for God to stop the "murderous hand" of terrorists and referred to the recent "abhorrent terrorist attacks" in Egypt, Britain, Turkey and Iraq, but did not mention attacks in Israel.
"The pope deliberately failed to condemn the terrible terror attack that occurred in Israel last week," a Foreign Ministry statement issued in Jerusalem said.
A July 12 suicide bombing in the seaside city of Netanya killed five Israelis. Islamic Jihad claimed responsibility.
"We expected that the new pope, who on taking office emphasized the importance he places on relations between the Church and the Jewish people, would behave differently," the Israeli statement said. It called on the pope to condemn attacks "against Jews in the same way he condemns terror attacks against others."
Later, Israeli Foreign Minister Silvan Shalom appeared to soften the criticism, saying he hoped the failure to mention the attack in Netanya "was a mistake and not a deliberate omission."
Vatican spokesman Joaquin Navarro-Valls, accompanying Benedict on vacation, issued a one-line statement saying the papal envoy "has already replied to the Israeli government." It did not elaborate.
Later, Navarro-Valls released a second statement in which he noted that Benedict's words expressly referred to terror attacks in "recent days."
"It's surprising that one would have wanted to take the opportunity to distort the intentions of the Holy Father," Navarro-Valls said in the statement. "Obviously the other week's grave attack in Netanya referred to by Israel falls under the general and unreserved condemnation of terrorism."
Benedict has issued a series of condemnations of terrorist attacks since the July 7 London bombings.
Speaking to reporters Monday at his vacation retreat in Les Combes, Italy, Benedict said he did not see an anti-Christian motive in the recent wave of terrorist attacks blamed on Islamic extremists, attributing them instead to "a much more general intention."
Benedict also said it was important to seek dialogue with the best elements of Islam.
After visiting a church, the pope brushed off a question about whether he believed Islam was a religion of peace.
"I wouldn't want to label (it)," he said. "Certainly there are elements that favor peace. It also has other elements."
Benedict said last week that terrorism is not the result of a clash between the West and Islam, but the action of "fanatics."
The pope's spokesman said Sunday that Benedict was placing immense importance on a meeting with Muslims in Cologne, Germany, while he is in his homeland next month to lead the Roman Catholic Church's World Youth Day. He also plans to visit a synagogue in Cologne that was destroyed by the Nazis and rebuilt in the 1950s.
Benedict served in the Hitler Youth organization as a teen and later deserted from the German army in the waning days of World War II.
Jewish leaders who have met with Benedict have given him high marks for his behind-the-scenes work to improve Catholic-Jewish relations during his years at the Vatican during the papacy of the late Pope John Paul II. He has also denounced the Nazi persecution of the Jews after watching a film on the life of John Paul that included graphic scenes of Nazis killing Jews and Poles.