The Crown Prosecution Service (CPS) sought a retrial after a jury was discharged in April following a 10-week trial.
The application was resisted by lawyers for the 74-year-old retired chief superintendent, who denies the gross negligence manslaughter of 95 fans.
The judge said: “I authorise a retrial of defendant David Duckenfield.”
Ninety-six men, women and children died in the crush on the Leppings Lane terrace at the FA Cup semi-final on April 15 1989.
Under the law at the time, Duckenfield was not charged over the death of the 96th victim, Tony Bland, as he died more than a year and a day after the disaster.
A retrial is expected to take place on October 7.
Court was adjourned until later on Tuesday for legal discussions.
In April, jurors at Preston Crown Court found former Sheffield Wednesday club secretary Graham Mackrell guilty of failing to discharge a duty under the Health and Safety at Work Act by a majority of 10 to two, but failed to reach a verdict on Duckenfield after 29 hours and six minutes of deliberations.
Mackrell, 69, who was safety officer for the club at the time, was accused of failing to take reasonable care particularly in respect of ensuring there were enough turnstiles to prevent unduly large crowds building up.
The court heard there were seven turnstiles for the 10,100 Liverpool fans with standing tickets.
Mackrell did not give evidence but Jason Beer QC, defending him, argued the build up outside was caused by other factors, including a lack of police cordons and the unusual arrival pattern of fans.
He was fined £6,500 and ordered to pay £5,000 costs for a health and safety offence related to turnstile arrangements on the day of the Hillsborough disaster.
Judge Openshaw, who presided over the trial, told the court before sentencing that if Mackrell had been sentenced according to today’s laws, the maximum penalty he would have faced would have been two years imprisonment.
However, his sentencing options were limited to those available in 1989 which were to give a fine.