Policing Minister Nick Herbert told MPs the move was necessary to allow officers to do their jobs without "one hand tied behind their back".
He said there was not enough time to wait for a Supreme Court appeal.
Police had regularly released suspects on bail for weeks, or even months in some cases, while an inquiry continued.
Senior police officers are due to meet Home Secretary Theresa May later on Thursday to discuss the issue.
'Dire' implicationsFresh guidance to police custody officers in England and Wales followed a ruling in the case of murder suspect Paul Hookway - involving Greater Manchester Police - by Mr Justice McCombe in the High Court in May.
It says officers will have to re-arrest suspects in order to detain or question them again beyond the four-day - or 96-hour - period - but may only do so with "new evidence".
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Danny Shaw Home affairs correspondent For over 25 years, since the Police and Criminal Evidence Act, it's been customary for officers to release suspects on police bail while they complete their investigations. Sometimes this can take weeks or months.
When the suspect returns to the police station, he or she might be detained for further questioning, rebailed pending additional inquiries, charged or released without action.
The ruling in the Hookway case has thrown this long-established practice into disarray. On the face of it, it means police have four days at most to bring charges - regardless of whether suspects are in custody.
The reality is that in thousands of cases this won't be possible. Police, under the new interpretation of the laws, will be powerless to prevent suspects walking away from a police station, with no conditions attached, unless they can find new evidence to arrest them again.
No wonder the Home Office and senior officers are urgently seeking a remedy.
The Association of Chief Police Officers' (Acpo) lead spokesman on the issue, Essex Chief Constable Jim Barker-McCardle, said there was "chaos and concern out there" after the ruling had "thrown the whole of policing into the air".BBC home affairs correspondent Danny Shaw said one senior police figure had described the implications of the court ruling as "dire" as it would have far-reaching effects on serious and complex cases where police needed time to gather evidence and speak to witnesses, such as in rape allegations.
Mr Herbert told the Commons that police "believe that the judgement will have a serious impact on their ability to investigate crime".
"It is likely that in most forces there will not be enough capacity to detain everybody in police cells," he said.
"In other cases it risks impeding the police to such an extent that the investigation will have to be stopped because the detention time has run out.
"The judgement will also affect the ability of the police to enforce bail conditions."
The minister said that with about 80,000 suspects currently on bail, the matter had to be dealt with urgently.
He said the emergency legislation would provide assurance to the police that they could continue to operate on the same basis, regarding bail, as they have for the last 25 years.
But for Labour, shadow home secretary Yvette Cooper criticised the government for only dealing with the issue now - despite Home Office officials learning of the Hookway decision in May.
Concern for victims"There has been considerable chaos in the Home Office around this, not just this week but for the last few weeks," she said.
Continue reading the main story 19 May: Judge rules orally against Greater Manchester Police, overturning 25 years of bail practice. GMP informs officials at Home Office soon after 17 June: Written version of judgement circulated among Home Office officials, Crown Prosecution Service lawyers and police chiefs who debate its implications24 June: Ministers alerted to the full scale of the problem. Association of Chief Police Officers commissions further expert legal advice 30 June: Acpo recommends emergency legislation. Ministers say it will be introduced "as soon as possible""Why is there still no clarity about what this means for the police? Some forces believe it affects custody but not bail conditions, others fear that it means bail conditions no longer apply."She added: "It is a deeply serious situation for the police, for prosecutions, and particularly for justice for victims."
Mr Herbert said that while the Home Office knew about the judgement last month, the full impact of it only became clear on 17 June.
The ruling was made by the district judge at Salford Magistrates' Court who said the detention clock continued to run while Mr Hookway was on bail.
Mr Hookway was arrested in November and police were given permission to detain him for 36 hours but he was released after 28.
Five months later, police applied to the courts to extend the period of detention from 36 hours to the maximum of 96 hours, but the district judge refused, saying that the 96 hours had expired months ago.
Greater Manchester Police sought a judicial review, but the ruling was upheld at the High Court.
The force will appeal to the Supreme Court on 25 July to have it overturned.
However Ian Kelcey, of the Law Society, said the courts may be sending out a message to the police.
He told BBC News: "Defence solicitors have been extremely concerned over the period of the past few years that bail has extended and extended, and I think this may be a message that's coming out from the courts that enough is enough and you can't just treat it as an ever-extending piece of elastic."
