Lord Justice Leveson has said that he will "hear every side of the story" about Jeremy Hunt's involvement in News Corporation's BSkyB bid before drawing any conclusions.
His press standards inquiry heard evidence suggesting that the Culture Secretary secretly backed the proposed takeover and leaked inside information to the media giant.
James Murdoch was questioned about a 163-page dossier of emails detailing contacts between Mr Hunt's office and News Corp director of public affairs Frederic Michel.
Lord Justice Leveson said: "I understand entirely the reason for some of the reaction to the evidence yesterday (Tuesday) and, in particular, to the emails about which Mr Murdoch was asked.
"But I am acutely aware from considerable experience that documents such as these cannot always be taken at face value, and can frequently bear more than one interpretation. I am absolutely not taking sides or expressing any opinion, but I am prepared to say that it is very important to hear every side of the story before drawing conclusions.
"In due course I will hear the relevant evidence from all the relevant witnesses, and when I report I will then make the findings that are necessary for me to fulfil the terms of reference that the Prime Minister set for me."
Lord Justice Leveson, a respected Court of Appeal judge appointed to chair the public inquiry, stressed he would take an impartial view of the evidence.
He said: "I shall approach the relationship between the Press and politicians from an entirely non-partisan judicial perspective, which I have no doubt is the reason that I was given this remit."
The Leveson Inquiry has a wide-ranging remit to examine the culture, practices and ethics of the Press, and make recommendations for the future regulation of British newspapers.
It has already taken evidence on unethical and possibly illegal behaviour by journalists, and on relations between police and newspapers. The inquiry is now turning to contacts between politicians and the national Press.