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.
MPs voted by 290-252 against a Labour motion calling for an investigation into Jeremy Hunt's handling of the BSkyB takeover bid.
Nick Clegg has laid bare a coalition rift by revealing that he wants the PM to launch a probe into Jeremy Hunt's handling of the BSkyB bid.
The Liberal Democrat leadership has asked its members to abstain in a debate over Jeremy Hunt's behaviour during the BSkyB bid process.