Under the compensation payout, John Paul College would receive about $9000, Mr Walsh estimated.
However, school losses associated with the problematic system were up to $25,000, he said.
Mr Walsh, who is also president of the Secondary Principals' Association, called the compensation package "an act of good faith", but warned it fell short of actual losses suffered by schools as a result of errors.
"It doesn't even touch the anxiety, humiliation and stress the teachers have suffered."
Rotorua Intermediate principal Garry de Thierry said his school would receive about $4500 under the package.
He applauded Mr Joyce for the offer, but said more needed to be done.
Many principals at rural schools, which had no administration staff, had taken time out to fix payroll problems, he said.
These schools would have dedicated a lot of extra hours to Novopay errors.
Mokoia Intermediate principal Deborah Epp, who is also head of the Rotorua Principals' Association, said the payroll system had fallen short in many areas.
However, reverting back to the previous Datacom system could prove problematic, she warned.
"Former Datacom staff are understood to have moved into other roles," Mrs Epp said.
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.
Mr Joyce said more staff had been recruited to deal with system botch-ups.
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.
