The 54-year-old music teacher threatened to shoot at police in a dramatic standoff that began on Thursday after officers sought to bring him to court.
Bern police said they arrested him and a woman after raiding an apartment building.
The man earlier failed to appear for hearings on Wednesday and Thursday telling his lawyer that he was suffering from “acute mental and physical exhaustion,” Blick.ch reported.
At the request of the court, officers went to the man’s apartment on Thursday but he refused to leave, shouting through the intercom for police to “get out,” the news site said, citing a witness.
He later appeared brandishing two samurai swords, according to media reports.
The man ran toward armed police in the garden outside his apartment building before returning to his apartment after he was pepper sprayed, 20Minuten said.
He later threatened to shoot officers, at which point law enforcement officials moved reporters away, put a security perimeter in place and police snipers took up positions.
The man subsequently remained in his apartment and reportedly poked his head out of a window, while a woman was seen in the same dwelling.
The standoff continued overnight with 50 officers surrounding the man's home, the Berner Zeitung reported online.
Meanwhile, the legal proceedings continued against the man in his absence.
The accused, a music school owner who reportedly dabbled in acupuncture, denies deliberately infecting 16 music students with blood from a pupil who was HIV positive between 2001 and 2005 as the prosecution alleges.
The man, who was released after being held in detention three times since 2010, is alleged to have acted under the pretence he was administering acupuncture.
In other cases he is accused of doping his alleged victims and infecting them by unknown means.
The prosecution, whose case rests mainly on the accounts of the victims, acknowledged that the motive for infecting the students was not clear.
The trial is expected to last three weeks.