The police watchdog said the South Yorkshire Police officers were all identified through the Jay Report, which found that more than 1,4000 children had been subjected to child sexual exploitation between 1997 and 2013.
In the report, Professor Alexis Jay criticises the way in which the force and Rotheram Council death with the complaints from teenage girls who said they had been raped and trafficked by gangs of mainly Asian men.
All together 13 officers had been referred to the IPCC, but three - who were identified through a separate internal review by the force - will not face investigation at this time.
The IPCC has decided that two do not justify an investigation at this stage and the status of the third remains under review.
IPCC Commissioner Kathryn Stone said: "The amount of public concern across the country about this episode and the impact on confidence in the police means it is important that a fully independent investigation is conducted to establish how South Yorkshire Police dealt with child sexual exploitation."
"I sincerely hope that victims and their families will see this investigation as a positive step towards answering the many questions they must have. I have met with South Yorkshire Police and am reassured by their commitment to fully cooperate with the investigation."
In one case, an officer is alleged to have argued during a child protection conference against incidents being treated as sexual abuse because he thought that the child had been "100 per cent consensual in every incident".
The Jay report was critical of the remarks, which related to a CID officer who had been investigating offences against a 12-year-old girl who had sex with five men.
The IPCC also said that there had been "no police activity" around a suspect who, according to intelligence records from June 2001, was threatening a family and encouraging a victim to engage in prostitution.
A spokesman for the watchdog said no officers have yet been identified in relation to this allegation.
Other allegations of misconduct centre on evidence in a 2003 rape case being lost and a failure to progress an investigation into a report of a 14-year-old girl being raped.
Two officers will be investigated over claims they failed to adequately investigate an incident of a young girl being found drunk in the back of a car, and an individual having indecent photographs of her on his mobile telephone.
In a further allegation, two officers will be examined over claims they did not adequately investigate naked images of a young girl and "possible evidence of group offending", the IPCC spokesman said.
The controversy following Prof Jay's report led to a series of high-profile resignations including Roger Stone, the Rotherham council leader; Martin Kimber, the council chief executive and Joyce Thacker, the director of children's services.
The most high profile resignation was that of Shaun Wright, South Yorkshire's police and crime commissioner, who was the Rotherham councillor overseeing children's services between 2005 and 2010.
South Yorkshire's chief constable David Crompton has also been under pressure to explain his force's attitude towards child sexual exploitation over the last 15 years.
Mr Crompton has pledged to investigate individual cases and stressed that his force has seen a massive increase in the number of officers and other staff devoted to tackling the crime in the last couple of years.
Last month, the the National Crime Agency (NCA) announced it would lead an investigation into outstanding allegations of child sex abuse in Rotherham.
The NCA said it was taking on the inquiry following a request from Mr Crompton.