The trio, two aged 11 and a 10-year-old, had been charged with arson over the blaze which swept through The Church of the Holy Name in Greenisland on September 1.
But criminal proceedings were ended before they were set to make their first court appearances.
The boys will instead be dealt with through a youth diversionary programme aimed at achieving a restorative outcome.
Police said the decision involved taking into account their ages and any views expressed by potential victims.
During the blaze an adjoining parish hall at the site on Station Road also went up in flames.
The fire, which destroyed roofing and caused extensive smoke and water damage to the Church of Ireland buildings, was not treated as a racially motivated hate crime.
All three boys had been expected to attend Belfast Youth Court on Monday for the first stage in the case.
However, it is understood that criminal proceedings against them were withdrawn last week.
There was no mention of the case during the court session.
In a statement issued tonight, the PSNI confirmed: “Three boys, two aged 11 and one aged 10, charged with arson in relation to a fire at a church and church hall in Greenisland on Sunday 1 will now be dealt with via a Youth Engagement Clinic for restorative outcomes.
“The decision was made following consideration and consultation with criminal justice partners, taking into account a range of factors, including the age of the children involved.
“The views of victims are also an important element in this Youth Engagement Process.”
The statement added: “Youth Engagement Clinics are a collaborative effort, led by the Police Service of Northern Ireland’s Youth Diversion Officers, involving the young offender, their parent or guardian, Youth Justice Agency representatives, and if applicable, the victim.”