The body which regulates health and social care in England admits it could have acted more quickly after a rape was reported at a home for people with learning disabilities in north London.
The rape is alleged to have happened in November 2015 and the home closed a year later.
An article in the Times on Thursday accused the Care Quality Commission of a cover-up.
The CQC says it will now investigate what should have been done differently.
The regulator said it inspected the residential care home, run by Hillgreen Care, following the alleged rape of a former resident, and carried out further inspections in January and March 2016.
At the same time, the incident was being investigated by the police - and this concluded in December 2016.
There was insufficient evidence for charges to be made, the Times article reported, because the victim was not able to speak and his clothing, containing potential DNA evidence, was washed soon afterwards.
Sir David Behan, chief executive of the CQC, said: "Whilst we did take action that led to the closure of this and two other services run by the Hillgreen Care Ltd, I believe that we could and should have taken action more speedily, both to ensure people were safe and in prosecuting this provider."
As a result, he said, he was commissioning an independent investigation, "which will report publicly to the CQC board and identify what has happened, what we should have done differently and which will make recommendations to strengthen our future work".
Sir David added: "We expect openness and transparency from those we regulate and we will hold ourselves to account to those same standards."
The CQC now has criminal powers to prosecute providers and individuals when people in their care have been harmed or placed at risk of harm.
It said it was "actively pursuing" what further action it could now take against Hillgreen Care.
A CQC inspection report from January 2016 found that the care home had serious issues with food safety, hygiene and cleanliness. There was also no registered manager in position in the home.
It concluded that "people were at risk because the service did not have effective systems and management oversight".
Hillgreen Care Ltd did not respond to the BBC's requests for a comment, but the Times said that solicitors for the company described many of the criticisms as "unfair and inaccurate".