In a heated Prime Minister's Questions, Ed Miliband asked why David Cameron had called in Sir Alex to investigate Tory chairman Baroness Warsi but not Jeremy Hunt.
The Prime Minister said: "There is a very significant difference between the two cases.
"In the case of Baroness Warsi there hasn't been a judge-led inquiry with witnesses, taking evidence under oath, to get to all of the factual evidence behind her case.
"That is why I asked Sir Alex Allan to look at that case and establish some of the facts of that case."
But Mr Miliband said it was not the job of the Leveson Inquiry to investigate alleged breaches of the ministerial code.