Home Secretary Theresa May said the report's "truly shocking" findings would be investigated in an inquiry led by Jon Stoddart, a former chief constable of Durham police, northeast England.
The new inquiry is a victory for the victims' families, who never accepted the official version of events and have campaigned for more than 20 years for "Justice for the 96".
The Liverpool supporters died after a crush in an enclosed, overcrowded terrace at the stadium in the northern city of Sheffield on April 15, 1989 during an FA Cup semi-final against Nottingham Forest.
The independent inquiry concluded in September that police tried to deflect the blame on to fans to cover up their own incompetence and suggested that 41 lives could have been saved if the emergency response had been quicker.
"The findings of the Hillsborough Independent Panel were truly shocking, but while the families have now been given the truth, they have not yet received justice," May said in a statement.
"I am determined to see a swift and thorough response to the findings of the Hillsborough Panel to deliver justice for the 96 football fans who died and the families who have fought so hard on their behalf."
The inquiry will focus specifically on the fans' deaths and will work closely with a separate police watchdog investigation into police conduct in the aftermath of the disaster, she added.
The watchdog will also receive new powers to investigate police misconduct, May said.
Stoddart, who stepped down from his top job in the Durham force this year, said his priority was to work with the victims' families.
"My role is to ensure that we determine exactly what happened in the lead up to and on the day of the disaster and establish where any culpability lies," he said.
Separately, Britain's High Court was considering a bid to overturn the "accidental death" verdicts reached at the original inquest.
The government's main legal advisor, Attorney General Dominic Grieve, applied to the court to quash those verdicts after the Hillsborough panel published its damning report.
