A QUEENSLAND church has been accused of covering up a parishioner's alleged sexual abuse of children, with a victim's father threatened with death if he went to the police.

Police believe senior members of the evangelical church, including a pastor, have been actively influencing parents and the child victims not to report sexual abuse to authorities over the past year.

Allegations of the cover-up emerged after a Brisbane Magistrates Court bail hearing for the accused abuser, who was involved with the church's youth choir and is facing 11 charges, including rape and indecent treatment of a child.

The Courier-Mail is prevented from naming the accused, who allegedly sexually abused four girls between 2010 and 2012, or identifying the church for legal reasons.

Police allege a pastor of the church failed to go to the authorities after a girl's father approached him in December 2012 claiming his daughter had been abused.

The pastor told the dad he would report the allegations to police, but never did, according to police.

Detectives allege members of the congregation were urged not to report the matters to police and believe a pastor made threats against those claiming sexual abuse.

The father of one of the girls was allegedly told he would be killed if he spoke to police.

The accused abuser was granted bail late in December subject to stringent conditions, despite police concerns he may flee the country or try to contact the alleged victims.

In granting bail, Magistrate John McGrath said the threat allegations were "of grave concern".

"Of grave concern to me is the allegation of the charge of threats and as I understand the allegations there, those threats were made and are directly referable to some of the charges," Mr McGrath said.

The accused's lawyer Christopher Hannay told the bail hearing his client was a "very well-respected'' member of the church, who "emphatically'' denied the allegations and was "terribly concerned and distressed'' over it.

"As I said, the issue's in relation to these allegations, because … substantial time has passed with the old ones," he said. "The fresh allegations, as I see, are some three years old and the earlier allegations are some two years old."

Mr McGrath granted the man bail subject to conditions. He must report to police daily and not be within 100m of the place where the choir is practising or performing.

The accused is due to reappear for a committal call-over on January 20.