"The coping mechanisms of the population, both resident and displaced, are being stretched to their limits."
MSF's report is drawn from evidence taken from medical teams and observers in the Mount Elgon region.
Rise in injuries
The army was deployed to the Mount Elgon region in March 2008 after reports that the SLDF was killing and raping civilians there, as well as looting properties.
The SLDF has extorted money from residents, under the threat of being killed or mutilated, according to the MSF report.
But Kenyan security forces have employed "ever more force to achieve their goals," in getting information on the SLDF, the group says.
A military operation which began in March 2008 was initially welcomed by the Mount Elgon population but violence in the region has since peaked, placing civilians in further jeopardy.
The Kenyan military is using indiscriminate violence against local men by the military, in what appears to be an attempt to extract information about the SLDF, MSF reported.
"Ever since the military came, the situation has become quieter. The military are solving the problem in one way, but in another way, not at all," one Mount Elgon resident interviewed for the report said.
"Now people are in the hospital or killed by the military. We worry because of the military now. They can just come, beat you and hurt you forever, even if you are an innocent person."
'Torture' in camps
MSF also says that since the military crackdown there has a been a sharp rise in the number of people requiring hospital treatment, with beatings being the predominant form of violence.
Many civilians said they were tortured while in military 'screening camps', where the male population of entire villages are held and interrogated.
Despite the military crackdown, the SLDF still has a strong presence in the Mount Elgon district.
"Although some currently portray the military intervention as a success, many in Mount Elgon District are convinced that the spiral of violence will continue as long as the causes of the conflict are not addressed," the report said.
"Even if many SLDF members have been killed or arrested, the group remains active in the district and the population still fears SLDF retaliation whenever the situation allows."
David Musila, Kenya's assistant defence minister, said the allegations that Kenyan army forces had abused civilians are baseless.
"Those allegations are very, very far from the truth ... Kenya has one of the most professional and disciplined forces in Africa, if not the world," he said.
"The military has helped the people, it has even helped restore peace and order in an area that had been devastated by the SLDF.
"Members of the public [in Mount Elgon] are happy and allegations of torture have not been proven."
More than 600 people have been killed and about 60,000 displaced since the SLDF began its campaign two years ago, human rights groups say.