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APNZ obtained information under the Official Information Act showing the ministry received 255 invoices from schools and school support staff for extra costs generated from administering payment errors.
The information also revealed school staff were owed $12 million as of the January 9 pay cycle.
The Secondary Principal's Association president Patrick Walsh said the ministry should pay the invoices immediately.
"We think those bills ought to be paid as a gesture of goodwill - they haven't ruled them out but Minister Joyce has said he wants to park that up until he solves the problems, but it does seem to us that we've had seven months of pain and we've got many more months of pain to come - the issue of compensation needs to be addressed now.
"Let's try and get some goodwill back for schools," said Mr Walsh.
Schools have not received compensation but in addition today (Wed) they have faced one of the worst days of errors in the six month history of Novopay.
Principal of Hora Hora School in Whangarei, Pat Newman, said this time the errors had extended to principals' pay.
"Myself along with every other principal in New Zealand were due to go up a grade level due to roll growth - but this hasn't been actioned, even though Talent2 had been instructed by the ministry of the full list of those principals and to action it," said Mr Newman.
Principals not being paid was one of a raft of new problems that Minister in charge of Novopay Steven Joyce signalled would plague the worst pay round since Novopay was launched in August last year.
He warned schools to brace themselves for what would be the toughest test on the system yet because of the changes to secondary teachers' pay rates as a result of the new secondary teachers collective agreement.
Mr Joyce described trying to fix the problems with Novopay as, "trying to change they tyre on the car when you're driving along the motorway at 100km/h".
He also described it as a "dog, with a few fleas".
The ministry hotline would take calls from school staff who can't contact school administration staff on Waitangi Day.
Mr Walsh preferred the description "a dead cat bouncing".
He said he didn't think the hotline would cater to the complexities school staff would phone in with.
He said the problems with Novopay would accelerate and there was no end in sight.
"The ministry report says this could go on for two years."
"Novopay has become a toxic brand in New Zealand and I think although we have to wait for a technical audit, it's probably done its day and they need to seriously look at another provider."