Under the compensation package, Nelson Park School should receive about $3000, Mr Bridge said.
That would probably cover about a fifth of the school's losses associated with payroll mistakes.
The compensation package was a step in the right direction, Mr Bridge said. "[But] it comes nowhere near the realities of what we're doing in terms of hours and the stress it's putting on the staff.
"Each pay you often have the same issue - you fill in the same forms, you ring the help desk and wait for an hour and a half and you get someone who can't help you."
The Secondary Principals' Association wants the error-ridden pay roll system scrapped. "Novopay has now become a toxic brand," president Patrick Walsh said.
"It's probably, in our view, better to bite the bullet, cut our losses and go back to Datacom."
He called the compensation package "an act of good faith" but warned it fell short of actual losses to schools as a result of errors.
"It doesn't even touch the anxiety, humiliation and stress the teachers have suffered."
The Post Primary Teachers' Association, which is seeking legal action for the "hurt and humiliation" caused by payroll problems, said the compensation offer had come too late.
"This didn't start six weeks ago - this started six months ago," president Angela Roberts said.
"We really had to force them to the table - this is the first thing they have done in seven months but it's great they have."
Mr Joyce said more staff had been recruited to deal with system botch-ups.
The technical review, performed by Deloitte, recommended system mistakes should be fewer than 1 per cent each pay round.
"In the past three fortnightly pay periods, the percentage of complaints and notifications received dropped from 2.2 per cent, to 1.9 per cent, to 1 per cent," Mr Joyce said.
Schools' payout:
The $6m compensation payout to schools includes $105 paid for each full-time teaching equivalent, plus $500 per school, meaning:
A small school with five teachers would receive $1025.
A large school with 120 full-time teachers would receive $13,100.