PC James Patrick had said crime figures were manipulated and sexual offences were being under-reported by 22-25%.
Last month, PC Patrick left the force after being subjected to disciplinary proceedings.
He called Sir Bernard Hogan-Howe on his LBC phone-in to ask if the Met were planning to overhaul their procedures on whistleblowers to avoid what he had to go through.
Sir Bernard responded: "We're always prepared to do that. Each case, as you will know sadly though your experience is not straightforward, so of course we're always prepared to look at that and if there's anything you can offer us in that, we'll try to learn.
"It's a difficult balance to strike."
Speaking about his resignation, Mr Patrick told the Commissioner: "I've had no choice, have I boss? "I felt very, very let down in particular by the senior levels of the Met."
Sir Bernard replied: "First of all, I'm sorry about your experience, because I'm sure whatever the rights and wrongs, you won't have enjoyed what you have gone through, nor your family.
"Secondly, I'm certainly happy to consider meeting if you would want to, now that the misconduct process is out of the way.
"And I hope you'd be prepared to accept as well that, although you've got a very firm view about what you've seen and your experience, I have asked for some independent advice to find out whether your allegations are endemic or in fact your experience was a one-off."
The Metropolitan Police Commissioner did admit that mistakes are made in the force's crime figures, adding: "None of our figures are perfect. We know that. We know that not all crime is reported. In terms of rape, it is thought that 85% of rape is never even reported, let alone recorded. The stats never tell us everything and errors are made."