Ms Hewitt said that as general secretary of the NCCL in the 1970s, she took responsibility for the mistakes that had been made at that time. It follows questions being raised over the historic links between the two organisations, with the PIE allowed to join the civil rights organisation as an affiliate member.
"I got it wrong on PIE and I apologise for having done so," she said in a statement.
Ms Hewitt said any suggestion that she had condoned or supported the "vile crimes" of child abusers was completely untrue.
However, she said: "NCCL in the 1970s, along with many others, was naive and wrong to accept PIE's claim to be a 'campaigning and counselling organisation' that 'does not promote unlawful acts'.
"As general secretary then, I take responsibility for the mistakes we made."