A court ruled on Tuesday on a high profile case that has drawn intervention from Pope Francis.
Judge Antonio Moreno justified his decision on the grounds that accused Catholic priests "responded directly to the archdiocese of Granada" and because the events allegedly took place at parish headquarters.
The judge said any financial compensation which the archdiocese must pay would be established at a later date.
Spanish authorities opened their investigation late last year after a 25-year-old man filed a police complaint alleging that he was sexually abused by several priests in Granada when he was an altar boy between 2004 and 2007.
He was aged 14 when he was first abused.
Pope Francis in November told reporters he received a letter documenting abuse from an alleged victim and called him, telling him to report it in person to the Granada diocese.
"I called the person and I told him, 'Go to the bishop tomorrow,' and then I wrote to the bishop and told him to start an investigation," the pontiff said.
The pope said the case caused him "very great pain, but the truth is the truth and we should not hide it."
A Spanish judge last January eventually charged ten priests and two laymen with "sexual abuse with penetration, exhibitionism, and concealment of evidence" involving an underage altar boy in the country's biggest ever clerical sex abuse scandal.
But a court later dropped charges against 11 of the suspects because the crimes fell within a statute of limitations of three years.
The judge left in place an indictment against one priest who was charged with the more serious crimes of "continued sexual abuse, with the introduction of a bodily member anally and attempt to introduce the penis."
The Archdiocese of Granada said in mid-November that it had suspended a number of priests pending the court probe.
The Archbishop of Granada, Francisco Javier Martinez, and several other priests prostrated themselves on the floor of the city's cathedral during a mass in November in a gesture of apology to victims of abuse.
Pope Francis has called for "zero tolerance" of sexual abuse by clerics and has said Catholic bishops "will be held accountable" for failing to protect children.