The Registrar of Companies, through an inspection audit last year and a series of income-tax audits since 2010, found the institution was not providing a clear picture of its accounts and not maintaining a list of properties. CSI Trust Association, incorporated as a religious and charitable company under Section 25 of Companies Act, faces various other allegations including making amendments to its rule book without the Centre's approval.

"The order for investigation was received just a week back," said a top official with the Chennai office of SFIO, on condition of anonymity.

The investigation is the culmination of a campaign -- starting in 2007 -- by church members who moved agencies from the local police in Coimbatore to the Prime Minister's Office to probe alleged fraud.

A report by RoC strongly recommended an SFIO probe in a January 2016 letter to the ministry of corporate affairs. The Prime Minister's Office on October 10 last year forwarded a petition seeking swift action to the corporate affairs ministry, providing impetus to the probe effort.

CSI is a part of the Anglican Communion and a successor in the subcontinent to the Church of England along with the Church of North India and the Church of Pakistan. It denies any wrongdoing. The RoC report found that "the subject company was filing different balance sheets with various statutory authorities with different information for the same financial year", according to Right to Information documents accessed by ET.

The RoC report lists a slew of perceived violations: alleged misappropriation of funds, concealment of facts in electing bishops, illegal sale of property and so on. As an instance, according to the RTI document, the church showed Rs 1,198.3 crore as total income in one annexure and Rs 1,317.3 crore in another for the same financial year.

"It appears the business of the company is carried out on a fraudulent/unlawful purpose," read the report. The fraud office, which has prosecuting powers, will consider possibilities of criminal conspiracy and diversion of funds for personal gain. The SFIO official added the probe will take a minimum of six months.

'RESULT OF BACKWARDNESS'

CSI is managed by a group of bishops called the Synod, who oversee affairs of 23 dioceses and carry out charitable work in over 16,000 villages. Including the Jaffna diocese in Sri Lanka, CSI has 24 dioceses and claims membership of more than four million.

The top trustee, the Moderator, is Rev. G Dyvasirvadam, who believes the special audit now undertaken by the income-tax department into the church's books for the period 2003-12 will prove it was not a case of deliberate fraud. "This is the result of backwardness, not corruption," Dyvasirvadam told ET by phone.

He said rural parishes have not been prompt in recording income and expenditure as part of their functioning, which resulted in delayed filings and some discrepancies.

"There was no fraud. Even if one diocese submits accounts with a delay, the entire church gets a bad name," he said, adding that purported irregularities happened before his time at the helm.

Dyvasirvadam has been Moderator, the chief trustee in the hierarchy, for the past two years. For members railing against the top order, the entry of Serious Fraud Investigation Office (SFIO) is a definitive step forward and a way around organised lobbying to thwart probe efforts.

"Because of my pursuit there are two cases on trial in courts and two in the investigation stage against bishops under CSI," said E Premkumar, a member of the church.

Another member, JS Rajkumar from Nagercoil in Tamil Nadu, who started filing complaints with agencies in 2009, said: "This case has moved forward despite continuous lobbying by the parties involved.

Looking forward, a fair inquiry into these complaints will expose all irregularities." Rajkumar is one of the 34 individual complainants in the case against the church.

END