Education director-general Sharyn O'Neill has directed schools to place more emphasis on teaching phonics in the first few years of school.
In a policy document designed to set Education Department priorities for next year, Ms O'Neill urged schools to "increase intensity of teaching and assessing mastery of phonics throughout the early years".
The department has been criticised in recent years for having a patchy approach to phonics, even though international research has found that explicit and structured teaching of phonics - the relationship between letters and sounds - is the most effective way to teach reading.
Ms O'Neill said references to phonics had been included in previous policy documents on the early years of schooling.
It had been included again in the Focus 2014 Directions for Schools to remind school staff of its importance.
"Every public primary school should prioritise phonics - it is very important for all children to build the foundations of literacy," she said.
"In some cases schools may find that children are struggling and if the teaching of phonics needs to be intensified for students to succeed, then we expect schools to do so."
Ms O'Neill said the "early years" referred generally to the first years of learning at school, but teaching of phonics would continue for as long as children needed it.
"We don't spell out a set number of hours," she said.
"It is up to teachers and schools to plan learning programs that best suit the students in their classes."
Federal Education Minister Christopher Pyne recently signalled the coalition's policy was to encourage a back-to-basics approach, with a strong focus on phonics and direct instruction, through improved teacher training.
The education document also urged schools to put a bigger focus on identifying and intervening where students were at risk of achieving below national minimum standards on national literacy and numeracy tests and to promote students' mental health.
Ms O'Neill said schools must also increase their emphasis on promoting safe and effective use of social media, "acting swiftly and strongly" when cyber bullying emerged.
Schools would have to manage within the budget allocation and staffing levels set by the State Government, she said, as they prepared for the introduction of a new "student-centred funding model" in 2015.