Between 2010 and 2012 six teachers applied for a maternity grant in such circumstances, the authority said.
In each instance, except one which the ministry said was granted in error, such applications were declined.
The ERA outlined the dispute, with the ministry saying a teacher was not entitled to a second maternity grant when she had not returned to work from an earlier period of maternity leave.
If a teacher were to be paid a grant on a second period of maternity leave, the amount would be nil as the teacher would not be generating income at the time.
The PPTA contested this and said the collective agreement contained no requirement that a teacher must return to work before entitlement to a second period of maternity leave was available.
It also said the payment of a maternity grant was not dependent on a genuine return to work between periods of unpaid maternity leave.
Authority member Michelle Ryan said the issue that needed to be determined was whether the ministry correctly interpreted and applied the provisions of the collective agreement.
She said she regarded the PPTA to be correct and said the ministry's approach was "mistaken".
She also ordered that the ministry calculate payment of a maternity grant according to the salary appointed to the position held by the teacher at the date of birth.
PPTA president Angela Roberts said the decision was a win for women.
"We are glad to get justice in that these are provisions in our collective agreement and it is always really great when we get a decision that supports members getting what they are entitled to.
Ms Roberts said she hoped other industries would follow suit.
"It would be great if there were more woman across the country who were better supported as they become mothers and also if there were other industries and employers, who could look at their woman and know there is a huge investment that has been made in these people and it's a sound economic decision to enable woman to go on leave and to come back."
"It's a win for women and for New Zealand," she said.
The Ministry of Education could see how the authority reached its decision but was still considering its response, head of student achievement Dr Graham Stoop said.
"Regardless of this, we are in the process of identifying school employees who might be affected by this decision and would like to work proactively with PPTA to ensure that all staff receive what they are entitled to."
Under the law a female employee is entitled to 14 weeks' payment for parental leave, which can be transferred to her spouse or partner. However, some employment agreements include their own parental leave provisions.
Extended leave of up to 52 weeks is available for employees with 12 months' eligible service.