Yates' comments come amid growing pressure on the News of the World and the Met police after a New York Times investigation accused the police of failing to follow up leads in the 2006 investigation.
Yates told the committee that "all reasonable steps" had been taken to warn individuals where police had reason to believe their phones had been hacked, which he said only applied in the case of 10 to 12 people.
He explained that police recovered between 91 and 120 telephone pin numbers from the list, but added that phone hacking is "very difficult to prove".
When asked by Labour MP Stephen McCabe about reports that nearly 3,000 phone numbers were uncovered by the original investigation, Yates admitting that the numbers involved were "confusing".
"We absolutely agree it is confusing. It has been confusing for us and the public, and it may be the case that we have to provide some level of reassurance around that".
Chairman Keith Vaz told Yates the committee would write to him following the session and decide what it wants to do next.
During the committee meeting Yates was also questioned about the relationship between members of the metropolitan police and journalists, following an admission by former News of the World editor Rebekah Brooks (née Wade) to the Culture, Media and Sport select committee in 2003 that the newspaper had paid police for information, shown in the below comments taken from a transcription of the report which followed.
"We have paid the police for information in the past," she answered. And will you do it in the future? (Ms Wade) It depends― (Mr Coulson) We operate within the code and within the law and if there is a clear public interest then we will. The same holds for private detectives, subterfuge, a video bag―whatever you want to talk about.
"It is illegal for police officers to receive payments? (Mr Coulson) No. I just said, within the law."
In his response to questions from the Home Affairs committee today, John Yates confirmed that it was illegal for police officers to be paid by journalists for information.
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