A presidential aide told AFP the soldiers would "deter relatives and friends of suspected and Ebola patients from forcefully taking them from hospitals without medical consent".
Ebola, a deadly tropical virus which causes severe fever and, in the worst cases, unstoppable internal and external bleeding, has claimed the lives of almost 900 people in four west African nations since the start of the year.
Sierra Leone has seen 646 cases, the highest number of any nation, and 273 deaths.
But the fight against its spread has been hampered by relatives discharging highly contageous patients and taking them back to die in their villages, where countless individuals may have contact with them.
"When patients are forcefully taken away, there comes the problem of transmission of the disease to others and this makes the issue of contacting-tracing difficult," a medic told AFP.
The presidency did not give exact numbers or locations for the deployment, but most of the country's Ebola clinics are in Kailahun and Kenema, the eastern districts hit hardest by the outbreak.
- President inspects health facilities -
President Ernest Bai Koroma toured health facilities being set up to combat Ebola in the capital Freetown on Tuesday.
A 20-bed treatment centre under construction the western suburb of Lakka will be the first in the city of 1.2 million, which reported its first Ebola case nine days ago.
Koroma urged builders at the clinic, which will include a sample-testing laboratory, to "speed up the facility, which is long overdue".
The president also visited a hospital to the east of Freetown but was but was denied access as three Ebola cases had recently been admitted, his office said.
Business returned to normal in the capital after a "stay at home" day called to give the authorities breathing space to reorganise the response to the outbrek.
Many shops were screening customers' temperatures with high-tech gadgets at their entrances while others provided chlorinated water and soap for customers to wash their hands.
"No handshakes please," read a poster on display at a bank in the central business district.
Health officials have been forced to issue warnings over the danger of excessive use of chlorine, however, following reports of people sipping solutions of the poisonous chemical and washing with it.
"It is detrimental to the user's health and can cause serious internal injury," health ministry spokesman Yahya Tunis said in a public announcement broadcast on television and radio.
"People should return to the traditional hygiene practice of handwashing with soap."