Jack Straw has told MPs he was not informed about allegations Labour MP Sadiq Khan had been bugged when his officials were told in December.
Jack Straw's officials knew about the bugging story, but he did not
Mr Straw said he was informed of press interest in a prison visit by Mr Khan but not claims the visit was bugged.
The Tories say Mr Straw's statement raised questions about the way the Justice department was being run.
An inquiry is probing claims Mr Khan's visits to Woodhill prison, in Milton Keynes, Buckinghamshire, were bugged.
Mr Khan, who made his name as a human rights lawyer before becoming an MP, visited his constituent and childhood friend Babar Ahmad in prison in 2005 and 2006.
The Sunday Times claims counter-terrorism officers secretly recorded the discussions - Mr Ahmad is awaiting extradition to the US which accuses him of running websites supporting terrorism, but faces no charges in the UK.
BBC Political Editor Nick Robinson said that privately officials admit that alarm bells should have sounded when they had a press enquiry about the bugging of a conversation involving an MP.
In a brief statement to the Commons on Tuesday evening, Mr Straw said he was not told about the allegations by his officials.
"I was aware, in December, of press inquiries from a newspaper concerning visits by my honourable friend the Member for Tooting (Mr Khan) to Babar Ahmed, but at no stage before last Saturday was I aware of any information that the press inquiries concerned any covert recording or anything like that," Mr Straw told MPs.
He added that there were a "wide range of other questions about this matter," which would be the subject of the inquiry he announced to MPs on Monday.
Shadow Justice Secretary Nick Herbert called on Mr Straw to make a further Commons statement "clarifying what he knew and when, and to provide any further information which he omitted to reveal yesterday (Tuesday)".
Mr Herbert asked why Mr Straw had not told MPs earlier that he had "known for some time there was an issue relating to Sadiq Khan and if officials knew about the covert recording, why did they not inform him earlier?".
He added: "There appears to be no control of the Ministry of Justice and MPs have been given partial information."
Mr Straw has ordered an inquiry into the alleged breaking of a 40-year-old convention known as the Wilson Doctrine, which forbids - or was thought to forbid - the covert recording of conversations between MPs and their constituents.
Shadow Home Secretary David Davis said confusion over the Wilson doctrine had undermined Prime Minister Gordon Brown's assurances last year that it would be upheld.
Life 'at risk'
Liberal Democrat justice spokesman David Heath said: "Jack Straw must come before the House as soon as possible and explain exactly what has been going on in his department."
Meanwhile, the ex-police officer who claims he bugged Mr Khan's visit to Mr Ahmad says his life is "at risk" after the case was leaked to the media.
Mark Kearney, a former police intelligence officer at Woodhill Prison in Milton Keynes, claimed the Met Police put him under "significant pressure" to bug Mr Khan.
He faces charges - unrelated to the bugging claims - of leaking information to a local newspaper.
Mr Straw announced on Monday that Chief Surveillance Commissioner Sir Christopher Rose is to head an inquiry into the allegations.
He said Sir Christopher, a former Court of Appeal judge, would try to find out under whose authority any bugging was carried out and would present his findings within two weeks.