The Democratic Unionist leader Arlene Foster has said the watchdog must stop favouring the "metropolitan liberal elite definition of equality".
Arlene Foster's criticism follows Monday's ruling that upheld that Ashers had discriminated against a gay activist for declining to take an order for a cake bearing the slogan "Support Gay Marriage".
Ashers' owners, Daniel and Amy McArthur, said that the message on the cake went against their Christian beliefs.
The commission spent almost £90,000 in legal costs in the court case against the Ashers family run bakery.
The McArthurs were found guilty of discrimination. That finding was upheld by the Court of Appeal in Belfast on Monday.
But the judgment did include some criticism of the Equality Commission.
It said the organisation should also have offered the McArthur family advice during the case, as the family believed their faith was also being undermined.
Arlene Foster said: "We have an enormous amount of sympathy for the McArthur family.
"We feel they have been through an absolutely horrific time - not helped I have to say by the actions of Equality Commission."
Commenting on the criticism raised in the judgment, she added: "I think the Equalities Commission need to have a long hard look at how they work with faith communities in Northern Ireland and instead of accepting the metropolitan liberal elite definition of equality they need to look at what real equality is and look at the faith communities in Northern Ireland and that is something they haven't been doing."