"Isn't it a fact ... that CusMod has to be there, because you don't want another Novopay to be running through the Customs system? That is what pretty much everybody in town is saying," Mr Shearer said, referring to the Ministry of Education's troubled payroll system.
Ms Tremain said that was not correct.
"This is a system that has over 2.7 million transactions through it, it has been operating for two years ... it doesn't have the hallmarks of a failing system."
In June 2012 it was decided to split the first stage of JBMS into multiple steps, because of the risk of problems if too much was transferred at once.
After her appearance, Ms Tremain rejected any comparison to Novopay, and said nothing was wrong with the system.
"I wouldn't change the roll-out at all, in fact, I think we have significantly de-risked it."
Ms Tremain said the extra money needed for the project had come from within Customs' and MPI's existing capital investment baselines.
She was "very satisfied" with the performance of IBM, and said the change to the governance group arrangements did not indicate any tension or problems.
"Originally the chair of the governance arrangements was a Customs person. Obviously we are balancing issues between Customs, MPI and what IBM want to do as our vendor, and sometimes having somebody who is neutral is a good thing."