Teachers say the move could result in the ministry having more input in teachers performance.
Currently teachers move up the pay scale by meeting professional standards set out in the collective agreement - principals assess and sign off on increases.
Under the ministry's proposal Mrs Longstone would be able to change the standards without consulting with teachers, or the union.
The Ministry did not respond to questions on the bargaining process, or their proposal.
NZEI National Secretary Paul Goulter said there was strong concern among members about the Government laying a base for the introduction of performance-based pay.
He said it could result in teachers' pay being linked to their students' National Standards results.
"So far they have all rejected the offer from the Government along with an outright rejection for Government's policy prescription for education reform in this country."
Mr Goulter said teachers had put forward their own proposal which they would not detail due to being in negotiations with the ministry.
He said the Government were pushing for a business model of education driven by cost-cutting and competition - the union has termed it the "GERM - Global Education Reform Movement".
He said policies being pushed this year were based on competition, data-based accountability and standardisation.
NZEI will hold its last paid union meeting tomorrow, after two weeks of negotiations with teachers.
APNZ understands the Post Primary Teachers Association are also in the collective bargaining process, but has managed to push similar proposals off the table.