WorkSafe prosecutor Dale La Hood told the Wellington District Court that the Ashburton office was open-plan, with no restrictions between staff areas and the public area.
Mr La Hood said controlling access into a staff working area was a key step the Ministry should have taken to ensure the safety of its employees.
In a statement Ministry chief executive Brendan Boyle said MSD was disputing the aspect of WorkSafe's prosecution relating to its interpretation of what a safe office layout should be.
"I do not accept that organisations working with the public need to do that from behind barriers," Mr Boyle said.
"We would never knowingly put our staff at risk. Ashburton was extraordinary in that Mr Tully was motivated to kill. Nothing can help someone intent on mayhem."
The Chronicle specifically asked the MSD if the Whanganui office was going to be open plan; if the Ministry saw that as posing any particular issues around client privacy; if there would be any special security arrangements controlling entry and exit of the building; and if staff and members of the public could be assured of their safety within the building.
The St Hill St office block is expected to be completed early next year.