The sexual attack reportedly took place in a shower room in the barracks in front of witnesses last Thursday night.
The victim, a kitchen soldier in his mid-20s, suffered scratches and bruises all over his body, the Blick newspaper reported on Wednesday.
The alleged attacker, a man in his early 30s, was arrested and questioned on Friday before being released.
“We have opened proceedings on suspicion of sexual assault,” army spokesman Tobias Kühne told Blick.
“The intensity of the attack is now clarified.”
A Thun training base commander Hans-Ulrich Haldimann appeared to be shaken by the incident.
“There has been nothing like this here ever,” Captain Haldimann told Blick.
“The exact reasons are still unclear,” he said.
“The alleged perpetrator was probably severely intoxicated on Thursday,” Haldimann said.
“We have sent him home”
The suspect’s basic training was set to end on Saturday.
The victim, meanwhile, is continuing his training.
“I have spoken to him personally about the incident,” Haldimann said.
“He told me he wanted to continue his service.”
The last time sexual impropriety in the Swiss Army hit the headlines was in 2008 when Roland Nef was forced to step down as head of the country’s armed forces over allegations of sexual harassment made by a former girlfriend.
Nef left after only seven months in the job.
The case with the girlfriend was settled out of court.