Winnipeg parishioners are in shock after learning approximately $400,000 was stolen from their church coffers over a period of five years.

Winnipeg police believe the theft at Saint Bernadette Parish to be an inside job.

This has parishioners feeling betrayed, says Pastor Fr. Phil Daley.

"It's a serious breach of trust, and I think the sense of betrayal is probably going to be quite high," he told CTV Winnipeg. "The money was collected, people got receipts for it, but it never made it to the bank."

Court documents show that the church's financial administrator is accused of embezzling money over a five-year period, starting in 2009.

The missing money became apparent during a routine audit conducted by the archdiocese in St. Boniface in May, 2015.

"It was not apparent at first," said archdiocese financial administrator Richard Frechette. "It's something that we discovered as we went along. The totals kept rising and rising and rising."

According to auditors, the thefts started off in small amounts. But by the end of the five years, they had risen substantially.

It is alleged that $120,000 went missing in 2014 alone. As well, $100,000 that was earmarked for church renovations also went missing.

Staff say the church ran deficits for years, with parishioners being asked to give more every week to make up for the shortfall.

Daley said the thefts have left many in the congregation feeling frustrated.

"They were frustrated because it just seemed that the more they tried, they kept getting the feedback that it's not enough," he said.

Leo McCaughan, the church’s former financial administrator, faces three charges related to theft, fraud and falsifying documents.

He quit his job a few months before the 2015 audit, telling colleagues that he planned to take a year off before looking for new employment.

McCaughan is scheduled to appear in court on Thursday.

With a report from CTV Winnipeg's Ben Miljure