Students started the first day of school with flares and smoke at two schools in Nicosia and Limassol as those at gymnasiums, lyceums and technical schools went back on Friday morning after the summer holiday.
People living near the Apostolos Varnavas lyceum in Strovolos called the fire service believing the smoke was caused by a fire.
In the morning, pupils at the Apostolos Peter and Paul school in Limassol also lit flares, causing the area around the school to resemble hooligalism at a football match.
Police and the fire brigade were called to the scene.
On Thursday, authorities reported partying ahead of the start of the school year would be policed.
The school district board gave headmasters the go-ahead to hire private security guards to patrol schools on Thursday night and even though numbers were reduced partying went ahead in a lot of locations and tradition banners unraveled by final year students were unveiled.
Students will on Friday be divided into classes, receive books and timetables and start classes, while pupils of elementary school will start on Monday.
During the current school year, 114 secondary schools will operate, of which 64 are gymnasiums, 38 lyceums, seven a combination of both and five evening secondary schools.
According to the education ministry, it is expected that a total of 39,980 pupils will attend, of which 22,991 will go to gymnasiums and 16,989 to lyceums.
A total of 2,006 permanent and 438 contract teachers have been employed, with another 80 contract teachers are expected to be appointed. The education ministry said it has taken all the necessary steps to reassign teachers to schools where they were previously teaching when possible.
Technical schools will be staffed by 550 educators. Currently there are 4,559 students in morning classes, 230 in evening classes, 195 apprentices, 293 students in post graduate educational and vocational training institutes and 90 in other units.