Michael Martin disclosed today that police did not have a warrant to search Tory immigration spokesman Damian Green's parliamentary office.
The Speaker told a crowded Commons that he "regretted" that a "consent form" was signed by Serjeant at Arms Jill Pay for the search.
"I did not personally authorise the search," he said.
A warrant will always be required in future for police to search MPs' offices, he said.
The seizure of material belonging to Mr Green will be referred to a committee of seven senior MPs.
Mr Martin's statement came after a furious political row blew up over the arrest of Mr Green and the searching of his offices in relation to a series of Home Office leaks.
Earlier today, Scotland Yard's acting chief Sir Paul Stephenson defended his officers' actions, saying detectives in any inquiry, no matter how sensitive, must follow the evidence "without fear or favour".
Home Secretary Jacqui Smith is expected to make a statement to the Commons tomorrow regarding Mr Green's arrest.
Mr Green was sitting behind Tory leader David Cameron as the Speaker rose to make his statement in a tense and crowded House.
Mr Martin said the arrest and search of Mr Green's office had caused "grave concern" to all MPs.
"In the past few days there has been much pressure on me to make public comment about these matters.
"But I felt it was right and fitting that I should make no comment until Parliament reconvened."
He said: "I should emphasise from the start that it is not for me to comment on the allegations which have been made against Mr Green or on the disposal of these allegations in the judicial process."
The Speaker reminded MPs that according to Erskine May, Parliament's rule book, parliamentary privilege had "never prevented the operation of the criminal law".
The joint committee on parliamentary privilege, in a report in 1999, had said the precincts of the House "are not and should not be a haven from the law.
"There is therefore no special restriction on the police searching the Parliamentary precincts in the course of a criminal proceeding."