Professor Nick Hardwick said he fully accepts there was a problem with the parole system, and that it was believed the victims had been informed before the decision was issued.
Speaking on BBC Radio 4's Today programme he said he is still trying to establish precisely what happened and does not want to "blame anybody yet".
He said it was not the Parole Board's responsibility to inform victims, and added: "Whoever's fault it was, I fully accept this was a problem with (the) parole system.
"I'm chair of the Parole Board, this would have been absolutely horrible for those two women concerned, and I apologise for it unreservedly."
London cabbie Worboys, a former stripper and adult film star, was jailed indefinitely in 2009, with a minimum term of eight years, for drugging and sexually assaulting women passengers.
In a statement, Prof Hardwick said he has "recently set out options for change" and that the Parole Board has a "statutory duty" under its rules which "prevents disclosure of proceedings".
"We will shortly be launching a public consultation about how we share our decision-making with the public," he added.
"I am very concerned some victims were not told about the decision; this must have been very distressing.
"There are robust arrangements in place for victims to be informed through the Victim Contact Scheme. We were told that had been done as usual in this case and released the decision on that basis."
Lawyer Harriet Wistrich said two victims had not been informed of Worboys' imminent release or of his Parole Board hearing.
She told the Press Association they are both "shocked and horrified by this news", and said on Channel 4 News that the first they learned of the planned release was while "listening on the radio, cooking tea for the kids".
It is understood that all those who were signed up to the Victim Contact Scheme were informed as soon as the Parole Board decision was made.
Yvette Cooper, chairwoman of the Home Affairs Select Committee, has called for the Parole Board to immediately publish its reasons for allowing the release of Worboys.
She said was "really shocked" by the move and called for scrutiny of the Parole Board's reasoning before the prolific sex attacker is let out of jail.
Worboys, who became known as the "black cab rapist", was found guilty of 19 charges of drugging and sexually assaulting 12 women passengers, in one case raping a woman.
But police said in 2010 that his alleged victims numbered 102 after more people came forward following his trial and conviction.
The allegations were investigated but no further action was taken on the advice of the Crown Prosecution Service (CPS), police said.
The director of public prosecutions at the time of Worboys' conviction, Labour's Sir Keir Starmer, has since urged any alleged victims with concerns about how their case was handled to contact the police.
Speaking outside his home in north London, the shadow Brexit secretary said: "First and foremost, it's very important that if there are any allegations that anybody thinks have not been looked into, sufficiently or at all, they go to the police and make those allegations so they can be looked into.
"The second important thing is that it's really important that what's said is factually accurate. As you know, the Crown Prosecution Service holds the file on this case, they made the decisions in the case, and it is really important you go to them to get an accurate read-out of the decisions that have been made."
Asked whether he thought the right decision was made by prosecutors not to pursue further allegations against the serial sex attacker, Sir Keir said: "I think these decisions were nine years ago and it's very important you go to the Crown Prosecution Service and get an accurate read-out of the decisions that were made, particularly if further allegations have been made now."
He refused to answer further questions about why past cases were not brought to trial.
It is feared Worboys may have more than 100 victims and the Parole Board's decision sparked an outcry from charities and support groups when it was made public on Thursday.
Charity campaigners have called the time served by the 60-year-old "woefully short" and said his release "beggars belief".
Meanwhile, Worboys' ex-wife, Jean Clayton, told the Sun he should "never be let out".
Ms Cooper said Worboys' crimes were "the most appalling and vile" and there were "serious questions" over the Parole Board's decision.
"Given the seriousness of this case, the Parole Board should publish their reasons immediately so both the decision and the process can be scrutinised before this man is released.
"We also need to know what information and support was given to all the victims before this decision was taken."
Her intervention raises the prospect that senior members of the Parole Board could be hauled before MPs for a grilling over the decision.