Members of a crisis negotiation team were deployed to the Stillwater correctional facility on Sunday.
A spokesperson for the state's Department of Corrections (DOC) said the reasons behind the incident "remains unclear".
But advocates say the move is in protest over prison conditions.
Excessive heat, limited access to showers and ice and unclean drinking water are among the reasons cited for the incident which took place in one of the facility's living units on Sunday.
Extra police units, firefighters and other emergency teams are stationed outside the facility in Baywater, about 25 miles (40km) east of the state's largest city Minneapolis.
A US National Weather Service heat advisory is in place until Tuesday for the area, warning temperatures could reach up to 100F (37.7C).
The increasing frequency of dangerously hot conditions has drawn renewed attention to US prisons and calls for reform.
Inmates have reportedly been on intermittent lockdowns since Friday because of staffing issues, meaning they are kept in their cells which reportedly do not have air conditioning.
AFSCME Council 5, the union which represents Minnesota correctional officers, said that understaffing was to blame for Sunday's incident.
A spokesperson said the incident was "endemic and highlights the truth behind the operations of the MN Department of Corrections with chronic understaffing".
Such conditions upset inmates because of restrictions placed on program and recreation time "when there are not enough security staff to protect the facility", they added.
The DOC says that two correctional officers are safe in the unit's secure control area. All DOC staff have been removed from the common areas of the unit currently occupied by prisoners.
The special operations response team had been deployed "out of an abundance of caution", a spokesperson said. adding the situation was "currently stable".
In total, about 1,200 inmates are incarcerated at the facility, according to department records.