A judge had given jurors a majority direction, meaning they did not have to unanimously agree a verdict, but they were discharged on Wednesday.
Mr Duckenfield was on trial alongside Sheffield Wednesday’s former club secretary Graham Mackrell, who was found guilty of failing to discharge his duty under the Health and Safety at Work Act.
Both men had denied the offences, almost 30 years after the disaster on 15 April 1989.
The jury deliberated for eight days, following a trial lasting 10 weeks at Preston Crown Court. The court told The Independent it would consider a retrial date on 24 June.
Mr Duckenfield, now 74, did not give evidence but attended the full case. The Crown Prosecution Service has indicated that it will seek a retrial.
The judge, Sir Peter Openshaw, had told jurors to be “dispassionate” and “objective” when considering their verdicts.
The victims were Liverpool fans who were in overcrowded pens at Hillsborough Stadium during an FA Cup semi-final.
The law did not allow prosecution over the death of the 96th victim, Tony Bland, as he died more than a year and a day after his injuries were caused.
Families of the 96 victims have campaigned for justice for 30 years.
Margaret Aspinall, chair of the Hillsborough Family Support Group, said: “We just have to wait and see what happens [with Mr Duckenfield’s second trial].
“I’d like to thank the jury for the weeks they’ve taken for their deliberations and I’d like to thank everyone for all the support we have had over the last 30 years. Hopefully that support continues.
“We were all hoping we would have some sort of closure today and we haven’t. We have still got a long journey.”
About 60 relatives who gathered at the Cunard Building in Liverpool gasped as the jury foreman told the court they could not reach a verdict for Mr Duckenfield.
But there were cheers as the guilty verdict for Mackrell was announced.
The 69-year-old, who was safety officer for Sheffield Wednesday at the time, was accused of failing to take reasonable care and ensuring there were enough turnstiles to prevent crowds building up while trying to get into the stadium.
There were just seven turnstiles for the 10,100 Liverpool fans with standing tickets, the court heard.
Mackrell did not give evidence but defence lawyer Jason Beer QC argued the buildup outside was caused by other factors, including a lack of police cordons and an unusual arrival pattern of fans.
The court heard that Mackrell was a former accountant with no health and safety training. He will be sentenced in May.
Prosecutors alleged that Mr Duckenfield, a former South Yorkshire Police chief superintendent, had “ultimate responsibility” at the ground on the day of the disaster.
The court heard he ordered the opening of exit gates at the Leppings Lane end of the ground at 2.52pm, eight minutes before kick-off, at the request of other officers amid dangerous overcrowding outside the entry turnstiles.
More than 2,000 fans entered through exit gate C once it was opened and many headed into a tunnel directly ahead, which led to the central pens where the crush happened.
Richard Matthews QC, prosecuting, told the court in his closing speech that Mr Duckenfield, who was promoted to the role less than three weeks before the match, should have had the knowledge to make “key lifesaving decisions” on the day.
But a defence lawyer argued that Mr Duckenfield had been “unfairly singled out” and that the case should not be considered with the benefit of hindsight.
Benjamin Myers QC told the jury the case was “breathtakingly unfair” and said Duckenfield had “tried to do the right thing”.
Sue Hemming, legal director of the CPS, said the trial had been “incredibly complex”.
“We have discussed the matter carefully with counsel and I can confirm the CPS will seek a retrial against Mr Duckenfield for manslaughter by gross negligence of 95 men, women and children,” she added.
“I recognise that these developments will be difficult for the families affected by the Hillsborough disaster. We have remained in regular contact with them throughout these proceedings, and spoke with those present in Preston and Liverpool before informing the court of our decision. We will meet with them shortly to answer any questions they have about the process.
“May I remind all concerned that criminal proceedings are ongoing and of the defendant’s right to a fair trial.”
Assistant Commissioner Rob Beckley, who leads the Operation Resolve criminal investigation into the Hillsborough disaster, said officers would “support the CPS as they prepare the case for future court hearings”.
“We recognise how challenging this process is for all concerned and will continue to keep people informed and updated, especially the families of the victims,” he added.
Liverpool FC said they “empathised with the frustration shared by everyone affected by the Hillsborough tragedy that the outcome was not definitive”.
“Our thoughts are with all those who continue to be affected by the Hillsborough tragedy and the 96 Liverpool supporters who went to watch their team and never came home,” a statement added.
In a joint statement, Steve Rotheram, the mayor of Liverpool City, and Andy Burnham, the mayor of Greater Manchester, said: “At long last, someone has been held to account for what happened – a vindication of the long-fought battle by families and campaigners for truth and justice.
“We welcome the decision of the CPS to request a retrial so that the issues of culpability can finally be resolved.”
Additional reporting by PA
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