From this question in the Lok Sabha,
"The proceeds of Primary Education Cess are credited to Prarambhik Shiksha Kosh (PSK) and are used to meet part of expenditure on SSA and Mid Day Meal (MDM) Schemes. There is no separate fund to credit Secondary and Higher Education Cess and funds required for secondary and higher education are directly allocated through budgetary provisions. State-wise data regarding utilization of cess is not maintained."
Why is this the case? Primary education cess collected in 2014-15 was around 36k crores. Therefore, higher education cess for the same year would be around 18k crores. The total higher education budget for that year was around 24k crore - which means only a 6k addition.