The tuition fee hike is being sought at the two federal institutes of technology in Lausanne (EPL) and Zurich (ETH) in the face of rapidly growing enrolments, the ATS news service reported.
The council of federal technology schools noted that the number of students enrolled at the two universities rose by 50 percent between 2004 and 2012.
Even with the planned increase, fees will remain heavily subsidized.
Students at EPFL and ETH currently pay 1,160 francs a year.
But the council said the average cost for educating a student ranges from 20,000 to 40,000 francs a year.
Nonetheless, students have protested the increases, arguing that they interfere with the right for post-secondary education to be available for all.
The administrations of EPFL and ETH have been tasked with leading discussions with student associations to explain the rationale for the fee hikes.