Peter Robinson says the commission needs to change
The DUP leader Peter Robinson has said the Equality Commission is "unrepresentative" of society in Northern Ireland" and must change.
He said only 34% of its staff are Protestant and none of the commissioners would "share the views" of DUP voters.
He said there is an opportunity to rectify the situation in September when four commissioner posts are filled.
The commission said it is committed to the needs of the whole community.
Mr Robinson was speaking after a meeting with the commission.
He said he will be pursuing the issue with the secretary of state
"The Secretary of State now has an opportunity to begin to rectify the perception that the Commission is totally biased against the pro-Union community.
"There are four commissioner posts to be filled in September," he added.
"This is an opportunity for the secretary of state to address the shameful past legacy of this body.
"I would strongly urge him to fulfil his legal obligations to ensure representativeness on the commission: something that has been absent up until now."
The commission is an independent public body which was set up in 1998 to take over the work of separate bodies dealing with fair employment, equal opportunities, racial equality and disability.
It is responsible for enforcing anti-discrimination laws.
It is led by Bob Collins, a former director-general of the broadcaster RTE.
In a statement a spokesman said the commission had clearly and publicly stated that "we want a workforce whose composition more fully reflects the society in which we live."
"As far as community background is concerned, the commission is doing everything that the law allows to increase successful applications from Protestants.
"That includes offering free, independent training on a religion-specific basis, exclusively for Protestants. This the first time that such a step has been taken by any employer in Northern Ireland."
He added that the appointment of commissioner are the function of the secretary of state and it would be inappropriate to comment on such appointments while a recruitment competition is in progress.
Sinn Fein's Martina Anderson said that while she accepted the point that "we must look at equal make-up and balance of many organisations" it was wrong to single out the commission.
She added: "The reality that Peter Robinson and the DUP must acknowledge is that all of the equality mechanism and safeguards flow directly from the Good Friday Agreement and Sinn Fein has made it very clear that these aspects are in no way up for sale."
SDLP equality spokesperson Alex Attwood said the comment were "reckless" and showed that Mr Robinson was attempting to "unpick the institutions of the Good Friday Agreement is an attempt to see off Jim Allister."