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Ms Longstone, who could be in for a golden handshake of up to $500,000, has been called a scapegoat for wider issues within the Ministry of Education.
Greens' co-leader Metiria Turei said the education secretary was taking the fall for what had been a "destructive" year for the ministry.
Ms Parata started holidays yesterday, and would not comment on the resignation.
Neither would Prime Minister John Key, who issued a statement to say he had complete confidence in his minister.
Ms Longstone spent little more than a year in New Zealand, making $560,000 in the first 12 months plus a $50,000 payment for moving from the United Kingdom.
State Services Commissioner Iain Rennie said he had spoken to Ms Longstone a month ago about her future and a decision was reached two weeks ago.
Mr Rennie said the relationship between Ms Longstone and Ms Parata had been strained and this extended to relationships between the ministry and wider education sector groups.
"There have been a number of strained relationships.
"Certainly the minister was one, but it was by no means one."
Mr Rennie said the troubles in education this year had been a tipping point in the relationship between the minister and Ms Longstone.
In a message to her staff, Ms Longstone said it had been an extremely difficult decision. "Not everything in 2012 has gone smoothly and there has been real disquiet relating to a range of issues including Budget 2012 proposals, Christchurch and Novopay.
"The accumulation of these and other things has led to deterioration in relationships with a number of important stakeholders - this isn't a sustainable position."
Calls for Ms Parata's resignation were started by the Opposition last week when the minister came under fire after a High Court decision found she unlawfully tried to close Salisbury School by disregarding warnings girls at the school with intellectual disabilities could be placed at greater risk of sexual abuse if they were placed in a residential boys' school.
Labour education spokesman Chris Hipkins said yesterday that Ms Parata should go.
"Hekia has been a disaster as education minister, everything she has touched she has stuffed up - from class sizes and school closures to Novopay and charter schools.
"Her tenure as minister has been a series of blunders, botch-ups and bungles."
Post Primary Teachers Association president Robin Duff said Ms Longstone was the "fall guy" for Ms Parata and Associate Education Ministers Craig Foss and John Banks. "She has been left high and dry."
Ms Longstone will go on a scheduled holiday to the UK, return on January 22 to complete her work at the ministry and stand down from February 8.
Her severance pay could be anywhere between $250,000 and $500,000.