Andy Coulson, 45, appeared at Southwark Crown Court on Thursday morning to face three charges.
Mr Coulson. who was News of the World editor between 2003 and 2007, pleaded not guilty to one charge of conspiring with others to intercept mobile phone voicemail messages.
He also pleaded not guilty to two counts of conspiracy to commit misconduct in public office.
The two charges allege that Coulson conspired with the paper’s former royal editor Clive Goodman – who yesterday also denied both counts – and others during two periods of time.
Mr Coulson spoke only to confirm his name and to enter his pleas, and was given bail as his case was adjourned.
He became deputy editor at the now defunt News of the World in 2000, before moving on to the position of editor three years later. He went on to become David Cameron’s director of communications and continued working for him after he became prime minister following the 2010 elections.
He resigned in January 2011 after allegations surfaced relating to phone hacking and bribery of public officials.
Ms Brooks, who used to run the whole British newspaper arm of Rupert Murdoch’s News Corp, stood beside her husband, Charlie, in the dock as they formally denied charges of conspiracy linked to the phone hacking scandal.
Also the former editor of the Sun and News of the World, Ms Brooks denied conspiracy to hack phones. It is also alleged that Brooks and her personal assistant Cheryl Carter, who also denies the charge, tried to remove boxes of archived material from the News International archive in 2011.
Former News of the World news editor James Weatherup, 57, from Brentwood, Essex, and former managing editor Stuart Kuttner, 73, from Woodford Green, Essex, also denied the charge.
The charges have emerged from Operation Weeting, Scotland Yard’s investigation into phone hacking and Operation Elveden, its probe into alleged corrupt payments to public officials.