Special forces were called in to help restore order at the prison in Tajikistan's second-largest city of Khujand after the riot broke out there on Wednesday, sources told AFP.
The penal facility houses prisoners serving long sentences for serious crimes such as murder and extremism including membership of the Islamic State group (IS).
One security source told AFP that the non-prisoners who died were a guard and a soldier.
A second source said that a further six guards had been injured.
"A riot involving dozens of prisoners occurred Wednesday night and continued into Thursday," one of the security officials told AFP, requesting anonymity.
The second source said the riot had begun when prisoners seized "cutting objects" from a workshop in the prison.
A funeral for the soldier and the guard who died in the clashes was planned for Thursday, one of the sources said.
The ex-Soviet country's government has yet to confirm the prison riot or the deaths.
Security beefed up at border
On Thursday the border service of Tajikistan's neighbour Kyrgyzstan said it had beefed up security near the countries' shared frontier because of the riot.
The border services of the two countries "have already discussed the situation in Khujand," spokeswoman Gulmira Borubayeva told AFP.
The prison in Khujand, located some 300 kilometres (185 miles) to the north of the capital Dushanbe, has seen violence and jailbreaks in the past.
In 2016, a guard and a prisoner were killed after three inmates initiated a jailbreak.
At the time the interior ministry said the prisoners had "planned to join the ranks of ISIS."
Tajikistan, a country of 8.5 million people bordering Afghanistan, has suffered severe conflict since it gained independence after the collapse of the Soviet Union in 1991.
Tens of thousands of people were killed in the country during a five-year civil war in the 1990s when rebel groups including Islamists rose up against the government.
Authorities in the majority-Muslim country have said that more than 1,000 Tajiks, including a high-ranking police officer who defected in 2015, joined IS in Syria and Iraq in recent years.
In July, an attack on foreign cycling tourists left four dead and two injured.
The assault was widely attributed to IS, although the government has refused to acknowledge the link.
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