John Yates has stressed his conscience is clear, in a defiant resignation statement.
He condemned "malicious gossip" that had been printed about him, telling him: "I have acted with complete integrity. My conscience is clear."
"It is with great regret that I make this decision after nearly 30 years as a police officer", he said.
"Sadly, there continues to be a huge amount of inaccurate, ill-informed and on occasion downright malicious gossip published about me personally. This has the potential to be a significant distraction in my current role as the national lead for Counter Terrorism."
He added: "I have acted with complete integrity and my conscience is clear. I look forward to the future Judge-led inquiry where my role will be examined in a proper and calmer environment and where my actions will be judged on the evidence rather than on innuendo and speculation as they are at present."
The assistant police commissioner resigned today after being pressured over his relationship with former News of the World deputy editor Neil Wallis, who was arrested last week.
Wallis was hired as a PR consultant for the police, an appointment which was cleared by Yates.
His resignation came as the Independent Police Complaints Commission announced it was investigating Yates due to his role in the phone hacking scandal and for nepotism.
The independent police body is also investigating Sir Paul Stephenson, the Metropolitan Police commissioner who resigned yesterday, and two other officers.