The party particularly wants assurances about remarks made by Hunt in a June interview with the Financial Times, in which he said that the takeover would not result in a "substantive change" to media plurality in the UK.
Last night, business secretary Vince Cable was stripped of the power to arbitrate on the Sky bid, after he told undercover reporters that he had "declared war" on News Corp chief Rupert Murdoch.
At a hastily-arranged media briefing today, Labour leader Ed Miliband confirmed that shadow business secretary John Denham would be writing to Sir Gus O'Donnell, the cabinet secretary, expressing concern about the way media powers were handed to Hunt.
"I think it is right that we as the opposition seek reassurance from Gus O'Donnell that he believes nothing that Jeremy Hunt has said has prejudiced him," said Miliband.
"There is material around what he has said about Sky and its role in the broadcasting ecology. That's why I think Gus O'Donnell needs to have a proper look through what Jeremy Hunt has said to make sure that he is satisfied that it doesn't create the same problems we saw with Vince Cable."
He added: "It was not a decision made at leisure it was a decision made in haste and the lessons of decisions made in haste is that they can unravel so it is right that we question that."
Lawyers have also questioned the legal basis for the government's decision to switch the powers between secretaries of state without primary legislation.