Lawrence Grech, an alleged abuse victim, spoke of the historic importance of his meeting with the Pope.
"I felt great and honoured, not even the president of Malta had the chance to meet privately with the pontiff," he told Al Jazeera.
"It was part of healing myself, I lost faith in God after my bad experience. I had the opportunity to meet with the pope and I saw that he was different from the media show, he showed me his soft heart about these cases."
The statement from the Vatican was one of the clearest yet that the church wanted local bishops to co-operate with civil authorities in prosecuting priests who abused children.
A spokesman for the Vatican said the pope met with the alleged victims as a group and then spoke to each individually before they prayed together.
"The Holy Father met a small group of persons who were sexually abused by members of the clergy," the statement said.
"He prayed with them and assured them that the Church is doing, and will continue to do, 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.
"In the spirit of his recent Letter to the Catholics of Ireland, he prayed that all the victims of abuse would experience healing and reconciliation, enabling them to move forward with renewed hope," the statement added.
It provided no further details of what measures would be implemented.
The pope's trip to Malta has been overshadowed by sex abuse allegations.
Earlier, at an open-air mass, he heard the island's leading bishop say the Catholic church had to be humble enough to recognise its failures.
So far on this trip, his first of five international visits planned for this year, Benedict has made no direct reference in public to the widespread allegations of abuses and cover-ups.
'Wounded by sin'
Speaking to reporters aboard the plane taking him to Malta on Saturday, his first foreign trip since the full scale of the scandals emerged, he said Roman Catholicism has been "wounded by our sins" but did not use the word "abuse".
"I know Malta loves Christ and his church that is his body and knows that even if this body is wounded by our sins, God still loves this church and his gospel is the true force that purifies and heals," he told reporters on the flight from Italy.
His flight to Malta on Saturday was one of the few to leave the Italian capital, Rome, amid the disruption caused by the Icelandic volcanic ash cloud.
Hundreds of cases of sexual and physical abuse of youths in recent decades by priests have come to light in Europe and the United States as disclosures encourage long-silent victims to finally go public with their complaints.
On the pontiff's first day in Malta, about 100,000 people - roughly a quarter of the nation's population - turned out to see him as he moved through the streets of the capital Valetta.
Benedict, in his earlier roles as an archbishop in Germany and later in his tenure at the helm of the Vatican morals office, has been accused by victim support groups of being part of a systematic cover-up by the church hierarchy of suspected paedophile priests.
The groups are demanding he take responsibility for the Vatican as an institution.
George Abela, the president of Malta, also discussed the issue at an airport ceremony welcoming the pope.
"It would be wrong in my view to try to use the reprehensible indiscretions of the few to cast a shadow on the church as a whole," he told the pontiff.
"The Catholic church remains committed to safeguarding children and all vulnerable people and to seeing that there is no hiding place for those who seek to do harm."
Abela called on the church and state authorities to work together so that "effective, transparent mechanisms are set up together with harmonised and expeditious procedures in order to curb cases of abuse so that justice will not only be done, but be seen to be done."