Because of the timing of the government's announcement last week, association president Jamie Stevens said Tuesday there is confusion about what the boards can do.
Under legislation, he said the deadline for boards to complete the closure process was March 31, but the province's request to put the process on hold was made three days later.
"So we're questioning whether or not we can put a hold on the decisions we've made," said Stevens.
Stevens said the boards are now wondering what can be done in cases where students are preparing to transfer schools and where teachers have applied for jobs at different schools.
The association wants the government to clarify its options.
"We're looking for a way that we can do that within the act and we are looking for guidance in that respect," said Stevens.
Education Minister Ramona Jennex put the process on hold, saying the review process used to close schools had become adversarial and upsetting for parents and the boards.
Jennex said she still expects to hear by April 30 whether boards have decided to comply with her request to suspend school closings.
"If there are issues around the budget and teachers and allocations then we will work with the boards to help them balance their budget," Jennex said.
She said funding will be provided from the province's capital budget for schools that need repairs to help them stay open, but no new money will be provided by the Education Department.
Four schools were slated for closure either this year or in 2014. Three are part of the Chignecto Central Regional School Board while one is administered by the South Shore Regional School Board.
Liberal education critic Karen Casey said money has to be found to help school boards adjust their budgets to keep schools open.
"They are going to take it from the classroom or somewhere else because it's not part of their budgeting process to fund those schools," she said.
Jennex has said that a discussion paper for public input on the school closing process will be ready this fall. A new process is expected to be in place next spring.