Slovenian army spokesman Simon Korez said the man, who worked as a military driving instructor in the northeastern town of Slovenj Gradec, was found dead at his home.
Korez said the man was thought to have shot himself with a rifle, which was however not military issued.
According to the 24ur.com news site, the 30-year-old took his life after having recently returned from psychiatric treatment.
Contrary to the suicide of the 27-year-old who shot herself while on duty as part of the Slovenian peacekeeping mission to Kosovo on Tuesday, the man involved in yesterday's suicide has never served abroad.
Korez said this was the first suicide committed by a soldier on the job in five years.
Explaining that the army was monitoring suicides among its members, Korez said that six service members had taken their lives in the past five years, but only one on the job.
Defence Minister Ljubica Jelusic and Chief-of Staff, Maj-Gen Alojz Steiner, expressed regret and conveyed condolences on the two deaths today.
Shock at the deaths was also expressed by deputies as the parliamentary defence Committee met to discuss the Kosovo peacekeeper's suicide.
Both Jelusic and Steiner assured the deputies that the two cases were unrelated.
The minister is worried that the two incidents could trigger further suicides, or rather "suicide threats, when people begin to use the threats to achieve their personal ends".
"We are getting ready for all possible scenarios, and have already taken steps to activate the psychological counseling services and instruct commanders to give more attention to soldiers," she said.
Steiner meanwhile stressed he could not connect the two incidents. "I can't explain why members of the Slovenia army are killing themselves," he said, adding that the suicide rate in the army is well below that in Slovenia in general.
Indeed, Slovenia is one of the countries with the highest suicide rate in the world. In the last decade, an average of 524 people took their lives every year. This makes for around 26 people per 100,000 inhabitants.
