The ministry also raised "serious concerns" about the health and safety risks of lightning strikes, which has led to application by the ministry in the Employment Court for an injunction against short-notice strike action.
The injunction application will be heard on Monday.
"We have taken this action as we feel we have been left with no other choice to ensure the safety of our staff, the public and the judiciary," the ministry's chief operating officer, Carl Crafar, said.
"The health and safety of everyone who works in or visits New Zealand's courthouses is our highest priority.
"We consider the PSA's decision to strike with only 30 minutes notice at crowded and busy courts to be unlawful, unsafe and irresponsible. We will do everything we can to protect everyone working in or visiting our courthouses."
It is another chapter in the ongoing discussions for a new collective contract which has seen the abrupt halt to trials and hearings in New Zealand's courts during the past few weeks.
On October 19, a strike shut down some of Auckland's District Courts with just 30 minutes prior warning.
PSA members, including court registry officers, victim advisers and Family Court co-ordinators, walked off the job in Manukau, Papakura and Waitakere between 2pm and 3pm.
Workers also gathered outside the High Court at Auckland on September 19 for a two-hour strike.
Ministry of Justice chief executive Andrew Bridgman has said bargaining on a new contract with the PSA has been on-going for several months.
The ministry has offered a 5 per cent increase over two years, in line with other agreements in the public sector.
However, the PSA wanted an increase of more than 13 per cent.
The union also wants to close the gender pay gap for ministry workers.
Crafar said the ministry has a budget of 3 per cent of its annual salary bill for pay increases this year and 3 per cent for next year.
"The ministry has also offered an additional $750 one-off payment to PSA members for 2018," he said.
"The PSA initially presented a pay claim which added up to more than 13 per cent during this period, more than double the Ministry's budget. They have subsequently reduced their claim to 11 per cent."