Wednesday's 14-hour prison standoff was sparked by prisoner protests over the detention of Islamic hardliners, including al-Qaida members, but ended peacefully with more than 10 hostages being released unharmed.
Officials said Jordan's government launched an investigation into what caused the riots and how to solve problems inside detention facilities.
Judge Ali al-Dhmour, the secretary-general of the Justice Ministry, said: "What happened in the prisons was very dangerous and we have to find out how the detainees coordinated with each other."
Al-Dhmour said the probe will look at whether detained hardliners at different prisons had passed messages using visiting relatives, the internet or mobile phones.
He added that the riots also raised concerns over Jordanian practices in dealing with prisoners, whether they are being held as individuals or as part of a hardline cell.
"We must review our regulations concerning how we deal with each group or case in the prisons" he said. "In the past, prisoners were all dealt with the same way, but what happened yesterday shows we have to thoroughly examine each group of prisoners to see if they should be dealt with differently."
Jordan's prime minister held talks on the riots early on Thursday with his justice minister and other officials.
Ibrahim Zeid al-Kailani, the former religious affairs minister, demanded greater insulation of ordinary criminals to prevent being influenced by Islamic hardliners incarcerated in the same prisons.
Al-Kailani said: "Many prisoners are depressed and frustrated ... so they fall under the influence of inmates who embrace the takfiri ideology, which brands other Muslims as infidels or other criminals."
Jordanian newspapers had little coverage of the prison riots and numerous officials declined comment.
"Many prisoners are depressed and frustrated ... so they fall under the influence of inmates who embrace the takfiri ideology, which brands other Muslims as infidels or other criminals"
Ibrahim Zeid al-Kailani,
Ex-religious affairs minister,
There were no evident signs of increased security at the Juweideh prison on Amman's southern outskirts where the hostage standoff occurred.
Hours after the riots ended, officials announced that police had arrested two Iraqi members of al-Qaida and a would-be Libyan suicide bomber who were planning to carry out a bombing in Amman.
It was unclear if the arrests and the riots were related, but they underscored that Islamic hardliners remain active in pro-US Jordan, which has prided itself on battling them.
Police are still searching for three Iraqis and a Saudi Arabian citizen belonging to the same al-Qaida cell.
The plot bore the hallmarks of the 9 November triple hotel suicide bombings in Amman that killed 63 people.
The causes of the riot remained unclear, but they focussed on at least two convicted al-Qaida members - including the killer of an American aid worker - being held at Swaqa prison, 102 km south of Amman, where too rioting broke out.
The third riot took place at Qafqafa prison, 100 km north of the capital.
Prisoners at Juweideh had demanded that the two al-Qaida-linked militants, Azmi al-Jayousi of Jordan and Salem bin Suweid of Libya, be transferred to their jail from Swaqa, an official said.
But an Islamic activist in Jordan said inmates began rioting after hearing reports that the two were being taken away for execution.