"According to initial results, this is not a case of infection caused by the Ebola virus," the Swiss Federal Office of Public Health said in a statement.
The office said that the man had arrived at an asylum centre in the western town of Vallorbe on September 17th, and had told officials that he had left Guinea for France two days earlier.
Officials at the centre acted fast because the man said he had lost a family member to Ebola, placing him in quarantine under watch from physicians.
After he began showing feverish symptoms on Tuesday, the authorities decided to transfer him immediately to Lausanne amid tight security.
The office stressed that the disease does not spread until the symptoms appear, and that there was no risk to the local population, saying the swift handling of the case showed the effectiveness of Ebola monitoring in the country.
Treatment of the Guinean came a day after a Geneva-based international aid organization flew one of its doctors to Geneva from Sierra Leone, after he was bitten by a child with the virus.
Initial checks showed the doctor is not infected, although he remains under observation at the Geneva university hospital (HUG).
The Geneva-based World Health Organization warned in a study released on Tuesday that the number of Ebola infections will triple to 20,000 by November, soaring by thousands every week if efforts to stop the outbreak are not stepped up radically.
"If we don't stop the epidemic very soon, this is going to turn from a disaster into a catastrophe," said Christopher Dye, the head of strategy at the WHO and a co-author of the study.
A day earlier the WHO said that the recent outbreak of Ebola in west Africa — the deadliest in history — has already killed 2,811 people.