Shocked parishioners at a Winnipeg church feel betrayed after learning hundreds of thousands of dollars has been stolen from them over a period of five years.

"It's a serious breach of trust and I think the sense of betrayal is going to be quite high,” said Pastor Fr. Phil Daley of the Roman Catholic parish of St Bernadette.

In court documents, the church’s financial administrator is accused of embezzling the money in 2009.

The financial issues became apparent during a routine audit by the Archdiocese of St Boniface in late May, 2015. The matter was reported to Winnipeg police two months later.

"It was not apparent at first. It was something that we discovered as we went along,” said Richard Frechette, financial administrator at the Archdiocese. “And the totals kept rising and rising and rising."

According to auditors, the thefts began with small amounts; however, after five years, the sums had risen substantially.

They allege $120,000 went missing in 2014 alone.

The church ran deficits for years with parishioners constantly being asked to dig deeper and give more to make up for the shortfall.

“They were frustrated because it just seemed that the more they tried, they just kept getting the feedback that it is not enough,” said Pastor Fr. Daley.

The missing funds include $100,000 earmarked for renovations at the church and the parish also had to cut back on charitable donations in Winnipeg and overseas.

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 audit, telling colleagues he planned to take a year off before seeking other employment.