The fresh investigation came after detectives were handed a new dossier of evidence hinting that suspicious activities at the News of the World went beyond "rogue" reporter Clive Goodman.
The now-defunct tabloid's royal editor was jailed along with private investigator Glenn Mulcaire in 2007 after they admitted intercepting messages.
Mr Mackey said: "Considerable resources have been dedicated to investigating phone-hacking and related offences and the officers on these operations will continue to follow all evidence of suspected criminality.
"The importance of the continuity of leadership will of course be taken into account when the future command structure for Operations Weeting, Elveden and Tuleta is considered."
Ms Akers told former Metropolitan Police Commissioner Sir Paul Stephenson she had planned to retire after the Olympics even before the new phone-hacking investigation was launched, according to the Independent on Sunday. She is believed to be the longest-serving woman in the Met.
A Scotland Yard spokesman said: "Deputy Assistant Commissioner (DAC) Sue Akers is due to retire later this year after 36 years service with the MPS.
"The DAC signalled her intention to retire this autumn when she took charge of investigations into phone-hacking and related corruption and computer crime."
Ms Akers, the former Borough Commander of Barnet, was awarded the Queens Police Medal for services to policing in 2007.