Paolo Gabriele was arrested May 23 after confidential letters and documents addressed to the Pope and others within the Vatican administration were allegedly found in his Vatican apartment.
Similar documents had been published in Italian media over the past several months warning of corruption, abuse of power and a lack of financial transparency at the Vatican.
Gabriele was being detained in a security cell on the Vatican grounds on charges of aggravated theft. The 46-year-old father of three is the only person charged so far after a nearly two-month Vatican-led investigation.
"As a father and a Christian, I hope the whole truth comes out to the beneficial advantage of the church," the detainee's father wrote.
His son "is personally paying the price of a situation that still isn't easy to understand," and won't be until the motive has been made public, he said.
"I hope above all that this tremendous sacrifice carries spiritual fruit" not only for those in a position of responsibility within the church, but for furthering the repeated desire of Pope Benedict XVI for the "necessary cleaning of the church," Andrea Gabriele said.
In his letter, the father sought to defend the younger Gabriele against the "distorted and often false and offensive" accusations being made in the media, which have accused the assistant of trying to harm the reputation of the church and Pope.
The letter came after a Vatican prosecutor decided to keep Gabriele detained beyond the usual 50 days according to Vatican law.
The Vatican spokesman, Jesuit Father Federico Lombardi, told reporters July 12 that Gabriele would probably stay in custody for another 10 days to allow the Vatican court to gather more evidence.
The Vatican court has questioned a number of witnesses, but none of them has been held or charged with anything, Father Lombardi has said.
The investigating judge, Piero Antonio Bonnet, is expected to wrap up the formal questioning process, which began June 5, and reach a conclusion by the end of July, the Vatican spokesman said,
The judge can decide whether to dismiss the case or have Gabriele stand in a Vatican trial that would be open to the public.
If Gabriele is ordered to stand trial, which would not begin before the end of September, he might be allowed to leave the Vatican detention cell for house arrest, Father Lombardi said.
Meanwhile, a commission of three cardinals recently wrapped up its parallel inquiry of the leaks and was due to meet with the Pope in mid-July to report its findings.
The papal commission, led by Cardinal Julian Herranz, 82, was established in March to investigate the leaked letters and documents; it reports directly to the Pope.
Father Lombardi said the commission, which includes 88-year-old retired Slovak Cardinal Jozef Tomko and 81-year-old retired archbishop of Palermo, Cardinal Salvatore De Giorgi, spoke with numerous members of the Roman Curia and other Vatican officials.
While the Vatican tribunal was to look into taking legal action against those who gave the documents to reporters, the cardinal commission was meant to help the Pope understand fully the reasons behind the leaks and the problems they appear to indicate.
The Vatican Secretariat of State was to carry out an administrative review of every Vatican office.