Sources earlier told BBC home affairs correspondent Danny Shaw that one wing of HMP The Mount in Hertfordshire and half of another wing had been "lost".
The Ministry of Justice (MoJ) later said the incident was "resolved" and no staff or prisoners had been injured.
A report into the jail published earlier highlighted staffing problems and said violence was an issue.
The Mount, in Bovingdon village near Hemel Hempstead, opened in 1987 and is classed as a category C male prison.
A "tornado team" made up of riot-trained staff arrived at the jail at about 18:30, equipped with shields and batons while fire, police and ambulance crews were on standby outside.
The MoJ said officers had dealt with an "incident involving a number of prisoners".
The BBC understands the wings involved were H and L, which house 110 and 117 prisoners.
At about 23:45, a Prison Service spokesperson said: "Specialist prison staff resolved an incident involving a number of prisoners. There were no injuries to staff or prisoners.
"The offenders responsible will be referred to the police and could spend longer behind bars."
Earlier on Monday, the Independent Monitoring Board published its annual review into conditions at Mount Prison and said it had "struggled" with staff shortages.
There were 24 vacancies out of a total of 136 officers in February, it added.
It also claimed violence "grew considerably" throughout the year and that drugs were readily available, in particular the synthetic cannabis substitute spice.
The report says concerns raised last year had not been addressed by the MoJ.
The Prison Reform Trust calls this type of institution one where "prison staff think [inmates] will not escape", while acknowledging they "cannot be trusted in an open prison".
Prison affairs academic and blogger Alex Cavendish had tweeted on Saturday: "Staff shortages at HMP The Mount (Herts) are so severe that this is the 3rd weekend of total lockdown. Meals given at cell door. Trouble brewing."
Mark Fairhurst, of the Prison Officers Association, said staff shortages in UK jails were "an epidemic" and partly due to "poor salaries".
"We need to increase the starting salary to incentivise people to join and then we need to give them regular increments to incentivise them to stay," he said.
Mr Fairhurst added it was difficult to retain staff because of "adverse working conditions, the violence they face and poor salary".
The Mount is built on a former RAF station site and has more than 1,000 prisoners, according to the MoJ.
It is described as a "hybrid training and resettlement prison" for inmates in the final six months of their sentences.
A 2015 inspection of the prison found The Mount was "reasonably safe and felt calm and well ordered", but chief inspector of prisons Nick Hardwick added that there was "room for improvement".
In March 2016 an inmate at The Mount stabbed a fellow prisoner with a shard of glass from a microwave.
Riot-trained prison staff were sent to a jail amid reports of violence on two wings.