These individuals were considered at risk and weeded out of the selection process even before basic training, army spokesman Christoph Brunner told the SDA news agency.
The number excluded last year rose to 1,213 from 965 in 2013.
Brunner confirmed a report that appeared on Sunday in the weekly journal Schweiz am Sonntag about the security checks, SDA said.
The checks evaluate the potential for violence of recruits, he said.
Those found to present a risk, receive neither military training nor arms.
The screening was introduced following an incident in 2007 at Zurich-Höngg, where a soldier used his assault rifle to kill a 16-year-old girl that he did not know at a bus stop.
The army said in April that it treated 41 cases of extremists among recruits last year.
Most cases related to individuals involved with extreme right-wing organizations but no major incident resulted, broadcaster RTS reported.
Only four cases related to jihadists and islamists and none of them resulted in criminal investigations, Brunner said.
The system of excluding recruits is based on evidence pointing to a potential radicalization and not on acts of violence, he indicated.