Court staff were briefed on the proposals this morning and were given access to a consultation document that suggested at least 96 jobs could go - a figure the ministry later admitted was wrong.
A ministry spokesman said the document has since been updated on its staff intranet.
Public Service Association national secretary Richard Wagstaff said the error was unacceptable.
"When an organisation consults with staff and their union about a number of jobs lost, one would expect it to be thoroughly checked and accurate because it affects people deeply and there is no room for those kinds of mistakes."
Mr Wagstaff said there would be "a lot of anxiety out there" and greater clarity would be welcome.
He said staff were reeling over the scale of the job losses and the level of change being proposed.
"People are upset. We know we had people literally in tears and they had to go home."
A Ministry of Justice spokesman said the consultation document contained "an error that overstated the amount of affected management positions and this has now been corrected".
The Government was responsible for court closure decisions while the ministry was responsible for those around staffing, the spokesman said.
The proposed changes would reduce the number of management layers and have minimal impact on frontline staff numbers.
Of the 1100 staff at district courts, fewer than 200 mostly management roles would be affected, the spokesman said.
The changes were proposals only, and staff and unions had known they were coming for some time.
"But today is the first time that most people have seen the detailed proposals, and decisions won't be made until we consult and get feedback from staff."
A spokesman for Mr Borrows said the minister's announcement would lead to 31 job losses, with the creation of 18 new jobs at other courts bringing the net loss to 13.
The minister's spokesman denied there had been a breakdown in communication with the ministry, saying the restructure was an operational matter for the ministry.
The changes come as the ministry aims to introduce new electronic systems aimed at streamlining criminal proceedings by next July.
They include the permanent closure of the Feilding and Upper Hutt courts, which have been temporarily closed since last year due to earthquake risks. The courts at Warkworth and Whataroa will also be closed.
Services at nine other courts will be scaled back significantly.
The Dargaville, Waihi, Te Awamutu, Te Kuiti, Opotiki, Marton, Waipukurau, Oamaru and Balclutha courts will be used only for specific hearings, rather than being open five days a week.
Other matters will be dealt with by post, telephone, online, audio-video link, or diverted to the nearest open courts.
Long-term decisions on the courts at Oamaru, Balclutha and Rangiora, which were closed last year due to earthquake risks, would be made next year.
Mr Borrows said the proposed changes - the first across the country's 63 district courts in 30 years - would come into effect early next year.
Law Society courthouse spokesman Iain Hutcheson said any decision to close or restrict hours at courts must ensure access to justice was maintained.
Green Party courts spokesman David Clendon said shutting courts in small towns was about saving money and would reduce access to justice.
Labour's justice spokesman Charles Chauvel said the changes would impact on the ability of ordinary New Zealanders to access the justice system.
