The Metropolitan police assistant commissioner John Yates has become the second high-profile Scotland Yard officer to resign over the phone-hacking scandal.

The resignation of Yates – the country's top counter-terrorism officer – comes a day after his boss, the Metropolitan police commissioner, Sir Paul Stephenson, stepped down.

In a statement, Scotland Yard said: "Assistant commissioner John Yates has this afternoon indicated his intention to resign to the chair of the Metropolitan Police Authority (MPA). This has been accepted. AC Yates will make a statement later this afternoon."

His decision to quit came as the Metropolitan Police Authority's professional standards cases subcommittee held a meeting to consider a slew of complaints against him.

The mayor of London, Boris Johnson, said the resignations of Yates and Stephenson were "regrettable but right". He said: "Whatever mistakes have been made at any level in the police service, now is the time to clear them up."

The MPA disciplinary committee, which met on Monday morning, announced that it had decided to suspend Yates pending an inquiry into allegations following the phone-hacking scandal.

Cressida Dick would replace Yates in the interim, Johnson said.

Green party MPA member Jenny Jones said the resignation should have happened earlier and left Johnson with a lot to explain.

"I think it's a real pity Yates did not go before his boss," she said. "It just shows who the most honourable person is. Boris has mishandled this from the start and he obviously has lots of questions to answer."

Earlier on Monday it emerged that Yates had been recalled to give evidence before the Commons home affairs select committee on Tuesday.

Keith Vaz, the Labour chairman of the committee, said: "The committee has recalled Mr Yates to give evidence tomorrow to clarify aspects of his evidence that he gave to the committee last week and following the statement of Sir Paul Stephenson."

When he appeared before the select committee last Tuesday, Yates expressed regret at his 2009 decision not to reopen the phone-hacking investigation. He insisted he had always told the truth to MPs investigating the issue and suggested that the News of the World "failed to co-operate" with police until the start of this year.

He told the committee: "I can assure you all that I have never lied and all the information that I've provided to this committee has been given in good faith.

"It is a matter of great concern that, for whatever reason, the News of the World appears to have failed to co-operate in the way that we now know they should have with the relevant police inquiries up until January of this year.

"They have only recently supplied information and evidence that would clearly have had a significant impact on the decisions that I took in 2009 had it been provided to us."

Vaz told Yates that his evidence was unconvincing and warned him it was "not the end of the matter".