A report, emails and memos acquired under the Freedom of Information Act, concern complaints of alleged bullying.

In a memo, a Department of Agriculture equality officer cites an independent report which found "sectarianism" and poor management practices "as being at the heart of most difficulties" in the agency.

She concluded: "As with other investigations there are issues which will need to be examined with Rivers Agency management and actions agreed to try and resolve the problems which run through the agency in Enniskillen and Omagh."

MEP Jim Allister said that since he publicly raised the matter a number of Rivers Agency employees had contacted him claiming to have been treated unfairly on religious grounds.

"I am discomforted by the failure of the departments of Finance and Agriculture to publish figures of the community breakdown of Rivers Agency staff members," he said.

"Clearly, there are deep problems within Rivers Agency, at the admission of its own departmental equal opportunities officer."

Arlene Foster, MLA for Fermanagh and South Tyrone, said she had written to the Agriculture Minister and Rivers Agency chief executive on behalf of around a dozen agency employees who contacted her but she was not content the matter was being given "sufficient impetus".

"There is a perception amongst workers that if a Protestant worker is disciplined and a Roman Catholic commits the same offence, a reason will be found not to discipline the Roman Catholic worker," she said.

"If the department's own equality officer says there is a serious problem and it is not being dealt with then what is the point of having an equality officer?"

Two employees who spoke to the News Letter said sectarianism was a problem within the agency.

A Department of Agriculture spokesman declined to comment on its internal documents, but gave assurances it had "robust policies and procedures in place for dealing with complaints of bullying and harassment".

"The department encourages all staff to report any incidents when they feel they have been mistreated, so that they can be investigated. All complaints that are raised by staff are treated very seriously and dealt with using agreed procedures," he said.

The News Letter asked for a religious breakdown of Rivers Agency's 422 employees under the Freedom of Information Act but the Department of Finance, which holds the data, refused on grounds of data protection and civil service rules.