Schools will now be required to formally notify the Department of Education if they are to use reduced timetables for pupils.
It follows a report earlier this month that found that shorter school days were being imposed on one in four children with special needs, mostly children with autism.
The report by Technological University Dublin and Inclusion Ireland found this was often done against the wishes of parents.
The department said the new rules would ensure that reduced timetables were only used where absolutely necessary.
Schools will now have to notify Tulsa's Education Welfare Service when putting a reduced timetable in place, explain why it is being used, obtain the consent of the parents and set out a plan for the pupil's return to a full school day.
The draft guidelines say reduced timetables should not be used as a sanction or a tool to manage behaviour and that it should only be applied as long as is necessary to facilitate a return to school on a full-time basis
The Department of Education said it would work with Tusla and the National Council for Special Education to ensure that where reduced timetables are being used its for time-limited periods only.
Parents will also be able to raise concerns about reduced timetables with their local Educational Welfare Officer.
Minister for Education Joe McHugh has invited schools and others working in the education field to help form new guidelines on reduced timetables and how they will be notified.
They have until 18 October to make submissions on the issue.