The Guardian's editor had criticised the order
Harriet Harman has warned courts off blocking journalists from reporting Parliamentary proceedings.
On Tuesday the Guardian said it was stopped from reporting an MP's question about an oil firm's injunction.
MPs have since raised concerns about so-called "super injunctions", which prevent reporting of both a story and the injunction itself.
Commons leader Ms Harman told MPs:"What is said in this House ... should not be subject to ruling by the courts."
The Guardian says it was initially blocked from reporting the question by Labour MP Paul Farrelly about an injunction obtained by Trafigura and its lawyers, Carter-Ruck.
The order was later changed and Carter-Ruck said there was "no question of Trafigura seeking to 'gag' the media from reporting parliamentary proceedings".
But several MPs raised concerns about it in the Commons on Thursday and are planning a debate next week on the "effects of English libel law on the reporting of parliamentary proceedings".
David Heath - Ms Harman's opposite number in the Lib Dems - asked that Justice Secretary Jack Straw be asked to address the debate in Westminster Hall, but Ms Harman suggested it might be upgraded and held in the Commons chamber.
She also said Commons authorities had known nothing about the Guardian order at the time.
Shadow Commons leader Sir George Young asked for "an urgent debate on press freedom ... so that honourable members can express their concerns that the freedoms won by [18th Century MP and journalist] John Wilkes will not be eroded".
Asked about the case in the Commons on Thursday Ms Harman said: "We will carry on doing our business and we will make absolutely sure that it is reported and it is not for the courts to stop that."
She said the matter was of "great importance" and said it was up to the Speaker, or whoever was chairing a debate, to decide what was said in the Commons.
"What is said in this House has got absolute privilege, the only control is the chair and that is exercised judiciously and always is and then what is said in this House can be reported so long as it is fair and truthful," she said.
"It can and must be reported by newspapers and other media outside and should not be subject to ruling by the courts."
At prime minister's questions on Wednesday Gordon Brown said the super injunctions were "unfortunate" and said Mr Straw was looking into it.