Martin Kimber appeared in front of the Home Affairs Select Committee to answer questions about the lack of arrests.
Chairman Keith Vaz asked why Rotherham had "failed so dismally".
Last year South Yorkshire Police's chief constable was criticised after The Times revealed police reports referred to widespread abuse of girls.
David Crompton was told to "get a grip" on the situation in Rotherham by the same committee in October.
South Yorkshire Police said it was working with agencies, including Rotherham council, on several investigations.
And in November the local authority said it had identified 58 young girls at risk of sexual exploitation in the town.
Mr Vaz told Mr Kimber not enough had been done since five Asian men from Rotherham were jailed in 2010 after being found guilty of grooming young girls for sex.
"In Lancashire there were 100 prosecutions the year before last, in South Yorkshire there were no prosecutions,"  he said.
"In 2010, an independent report described the localised grooming offences prosecuted in Rotherham as being at the top end of seriousness.
"We're talking about hundreds of victims, of vulnerable young girls, who have not been protected because, at the end of the day, what people are looking for are prosecutions."
Mr Kimber said: "I would certainly apologise to young people and families that have been let down.
"I don't think that it is ever as a consequence generally of individual failures, it's nearly always systemic failures."
Joyce Thacker, director of children and young people's services at Rotherham Metropolitan Borough Council, also faced questions from the committee.
She said: "I don't think we'd fully accept we've failed dismally to deal with the issue."
"When you look back at practice from, say a decade ago, things have substantially improved in that period of time."
The abuse of young girls in Rotherham, and also in Rochdale, Greater Manchester, came to light after a series of investigations by The Times.
The newspaper claimed documents it obtained show agencies were aware of extensive and co-ordinated abuse of white girls by some Asian men in Rotherham for which no one has been prosecuted.
The chief executive of Rotherham council has apologised to victims of child sexual exploitation who have been "let down" by its "systemic failure".