Police have fired tear gas in separate clashes with striking prison warders in the northern city of Mzuzu and the eastern city of Zomba.
Junior prison staff are staging a nationwide strike to demand improvements in their work conditions and have closed entrances to jails.
The government decided to send police officers to all prisons to watch over inmates, a move that was resisted by the striking warders.
In Mzuzu, prison warders fired shots in the air forcing the police to flee and fire tear-gas canisters from a distance.
The police in Zomba were also chased by the strikers who threatened to fire live bullets.
Prison warders are demanding to be given a risk allowance, improved working conditions, an end to alleged nepotism and fair treatment when granting promotions to staff.
Malawi’s Times Media Group tweeted a photo of the situation in Mzuzu: