The Franciscan order of Friars Minor has announced it is in grave financial difficulty after the discovery of a massive fraud.

An internal investigation begun four months ago has found that some friars who ran the Franciscans’ endowment engaged in “questionable financial activities” that have emptied the 800-year-old order’s coffers.

The Franciscans are a community within the Catholic church who follow St Francis of Assisi, who was known for advocating a life of poverty.

The order’s financial woes were disclosed in a rare open letter published this week by American friar, Michael Perry, the Franciscans’ minister general.

He painted a desperate picture of an order whose viability is in doubt and facing a “significant burden of debt” as a result of the deception. He also cast blame outside the church. “These questionable activities also involve people who are not Franciscan but who appear to have played a central role,” he said in the letter.

While short on detail, the letter describes an investigation that began in September into the activities of the office of the general treasurer of the Franciscan order dating back to 2003. An unnamed general treasurer has resigned from his duties, Perry said.

The inquiry so far has discovered that the Franciscan order is facing “grave, and I underscore ‘grave’ financial difficulty”, Perry said and that the systems of oversight meant to protect the order had been either “too weak or compromised”.

“We are encouraged by the example set by Pope Francis in his call for truth and transparency in financial dealings in the church and in human societies,” Perry wrote.

He added that civil authorities were also involved in the case, since outsiders were considered at least partly to blame for the alleged wrongdoing.

The church was also seeking the advice of outside lawyers.

The Franciscan order declined to comment.

The Vatican bank is also mired in investigations including allegations of shady property deals. Pope Francis has called on the Vatican bank to be more transparent and accountable as part of his effort to reform the church’s bureaucracy.

• This article was amended on 22 December 2014. An earlier version referred to monks throughout, rather than friars, and the original photograph showed friars from a different Franciscan order, the Capuchins.

