The pope met privately with eight Maltese victims of sexual abuse in the Vatican's embassy in Valletta.
A statement issued by the Vatican after the meeting said he prayed with the men and assured them the Church will continue doing all in its power to investigate allegations, to bring to justice those responsible for abuse and to implement effective measures designed to safeguard young people in the future.
The statement was one of the clearest yet from the Vatican that it wants local bishops to cooperate with civil authorities in prosecuting priests who abused children. It also stated the pope was deeply moved by the stories of the abuse victims and expressed his shame and sorrow over what they and their families have suffered.
Lawrence Grech was one of the abuse victims who met with the pope. He said he lost his faith 20 years ago, but this experience will change his life.
"I am more than satisfied," said Grech. "I cannot explain. It is more than I expected, because to meet the pope personally you have to be something special."
Grech is now married with two children. He started a legal battle against the Church in 2003 for which he said he would continue to raise awareness.
Before the meeting Pope Benedict celebrated a large open-air mass in Valletta, attended by thousands of people.
The pope's last event in Malta was a meeting with young people on Valletta's waterfront, where he arrived by boat. He told the youth that today's culture promotes ideas and values that are different from those of Jesus. It is easy when one is young and impressionable, the pope said, to be swayed by peers to accept ideas and values that do not belong to Jesus.
Malta's society, the pope said, is steeped in Christian faith and values.
"You should be proud that your country both defends the unborn and promotes stable family life by saying no to abortion and divorce," said Pope Benedict.
Pope Benedict's visit to Malta was aimed at commemorating the 1,950th anniversary of the shipwreck of Saint Paul on the island.