“As the matter is ongoing it is not appropriate to comment further.”
Mr Jabbour was appointed as deputy commissioner of capability in September 2015 for a five-year term after holding a range of senior posts.
When Mr Jabbour was elevated to the senior position, then-justice minister Michael Keenan praised his years of “distinguished service” and extensive experience across community policing, organised crime and counter-terrorism.
Having started with the AFP in 1990, he is now one of four deputy commissioners who report directly to commissioner Andrew Colvin.
Mr Jabbour was last in the headlines over his role in investigating Mr Haneef, who was wrongly charged and detained in 2007 for suspected terror links.
A 2008 report from retired NSW Supreme Court judge John Clarke found that Mr Jabbour was “unable to see that the evidence he regarded as highly incriminating in fact amounted to very little”.
Mr Clarke said Mr Jabbour was “impressive, dedicated and capable” but had lost objectivity as he persuaded reluctant British police to arrest Mr Haneef.
There is no suggestion the internal investigation revealed on Thursday is in any way related to the Haneef matter of 12 years ago.