The Ministry's offer, which would have amounted to $569 million over four years, would have seen the principal of a school of fewer than 50 students increase their roll-based salary component from $81,553 to $92,976 by 2020, plus a $2320 leadership payment.
Teachers at the top of the scale would have earned $82,992 a year by 2020.
The offer would also have increased the starting salary of new teachers, who currently start on $47,980, to $50,902 from mid next year, to $52,429 in 2020.
NZEI members took part in a secret online ballot, which closed on Tuesday night, to decide their views on the Ministry's second offer.
NZEI Te Riu Roa President Lynda Stuart said members had sent a clear message that the offers did not address concerns about the growing teacher shortage, time to teach and support for children with additional learning needs, all of which have been central to NZEI's collective bargaining position this year.
“Teachers and principals are saying that they are disappointed by the Government's failure to deliver and they are resolute in their determination,” Stuart said.
“The Government keeps saying we have to be patient, and they can’t fix everything at once, but the teacher shortage is at crisis point.
"If you think it’s expensive trying to fix a crisis, just wait to see how hard it is to turn around a disaster.
"In the meantime, our students’ learning suffers when we can’t even find relievers to cover for sick teachers."
Stuart said members are now discussing what steps to take next - including the potential for a second teachers' strike.
“At the NZEI Te Riu Roa Annual Conference at the end of this week, representatives will consider the compiled feedback about potential collective action and will make a recommendation about what we do in Term 4.
"If further strike action is recommended, all affected members will vote on this early next term," she said.
The offer was presented prior to the release of a Draft Disability and Learning Support Plan by Acting Minister of Education, Tracey Martin, last Friday.
The draft includes a proposal for an in-school Learning Support Coordinator role, however funding has not yet been committed.
Responding to news of the rejection, the Ministry of Education's Secretary of Education, Iona Holsted, said the Ministry was disappointed.
"The Ministry will continue to work closely with the NZEI Te Riu Roa to discuss its feedback to the details of the package, which delivers increases of 9.3 per cent over three years and which is valued at $569 million over four years," she said.
She said that the Ministry was working outside the bargaining process to address some of the concerns teachers had raised about working conditions, including measures designed to increase the number of teachers and the removal of National Standards.
"Budget 2018 includes $20m over four years to increase teacher supply, $370 million for 1500 new teacher places by 2021 to meet population growth and $59 million for teacher aides," Holsted noted.
According to the Ministry, primary teacher retention rates are over 90 per cent.
The Ministry is also currently working with teachers to plan a long term education workforce strategy, Holsted said.