John Yates, who has resigned as Metropolitan Police assistant commissionerCredit: Lewis Whyld/PA
Yates' resignation comes a day after assistant commissioner Sir Paul Stephenson also stepped down.
Following a discussion today, the Metropolitan Police Authority (MPA) said it had decided it would be right to suspend Yates pending a referral to the Independent Police Complaints Commission.
But in a statement, the Metropolitan Police confirmed that Yates had indicated his intention to resign to the chair of the MPA and that it had been accepted.
Yates is due to make a statement later today. Stephenson's resignation announcement yesterday followed criticism of the Met's hiring of Neil Wallis, the former executive editor of the News of the World, as a PR advisor in 2009.
Wallis was arrested last week by officers investigating allegations of phone hacking.
This morning, London mayor Boris Johnson said there were also questions over Yates' relationship with Wallis, which he suggested the MPA would be discussing today.
In a press conference today chair of the MPA Kit Malthouse said there had been "an accumulation of issues that was causing a problem".
Today Yates was also recalled by the home affairs select committee after giving what committee chair Keith Vaz called "unconvincing evidence" on phone hacking last week.
The committee is also due to hear evidence tomorrow from the now ex-Metropolitan Police commissioner Sir Paul Stephenson and director of public affairs and internal communication Dick Fedorcio.
Yates has been recalled to "clarify aspects of his evidence that he gave to the committee", Vaz confirmed today.
Update: Later in the day home secretary Theresa May confirmed that Cressida Dick will take over as assistant commissioner.