Born in 1959 in Jayapura, Papua, Karma was raised in an upper-class family active in local politics. His father, Andreas Karma, was a civil servant educated by the Dutch who had continued to work in the Indonesian government after independence, serving as a regent of Wamena, and Constant Karma, one of Filep Karma's cousin, served as deputy governor of Papua.
Filep Karma was influenced as a child by a midnight raid on his home by Indonesian soldiers who broke the family's furniture. He later studied at Sebelas Maret University for a time in Solo, Java which he earning undergraduate degree and becoming a civil servant like his father. In 1997, he traveled to Manila to study for a year at the Asian Institute of Management. He was unable to finish his studies.
Karma has two children.
When Karma returned from Manila, he found Java engulfed in protests against President Suharto. He became involved in the movement and began advocating the secession of Papua from Indonesia.
On 2 July 1998, he led a ceremony to raise the West Papuan flag in Biak, following which, activists clashed with police, resulting in injuries to a dozen officers. The Indonesian military occupied Biak Island four days later and fired on the activists; Karma has alleged that more than 100 protesters were killed and buried on nearby islands, though a precise death toll is unknown. Human Rights Watch protested the Indonesian government's actions, noting that in the months that followed, it "continuously failed to carry out a serious investigation of these incidents, or hold accountable the perpetrators of abuses against the people in Biak". Karma himself was wounded in both legs by rubber bullets. He was then arrested, tried, and sentenced to six-and-a-half years' imprisonment for treason; the sentence was overturned on appeal after Karma had been in prison for ten months.
On 1 December 2004, he participated in a second flag-raising ceremony, marking the anniversary of Papuan independence from the Dutch. Indonesian security forces were again alleged to have fired into the crowd, killing pro-independence activists, and Karma was again arrested on charges of treason against the Indonesian state, this time along with fellow activist Yusak Pakage.
At Karma's trial, the judge mocked his Christian beliefs and gave him triple the sentence that the prosecution had requested. Karma is serving this fifteen-year sentence in Abepura Prison in Jayapura. Pakage was imprisoned on a ten-year sentence, which he served until early release in 2010. After the trial, Karma's lawyers reportedly found a dog's severed head on their doorstep accompanied by a note reading "Kill Karma".
In August 2008, 40 members of the US Congress sent a letter to Indonesia calling for Pakage and Karma's release, in response to which a 100-person rally protested in front of the US Embassy in Jakarta.
In 2009, the Asian Human Rights Commission stated that guards had beaten Karma for returning late from a prison leave on 1 February, breaking his glasses and tearing one of his eyelids. In 2010, Karma was allowed to give an interview to a local radio station, in which he stated that he had been regularly abused by prison authorities: "I have been punched, kicked, pulled. But what hurts more is the mental torture we are subjected to." A spokesman for Indonesia's Foreign Ministry responded to the BBC News that "allegations of prisoner abuse were always investigated and dealt with properly."
In May 2010, prison officials denied the request of Karma's doctors to take him to Jakarta for proper medical treatment, and Amnesty International again issued an alert for his safety. In December 2010, Karma was transferred to a Jayapura police station following a riot at the prison, causing Human Rights Watch to reiterate its call for him and his fellow political prisoners to be freed, and to protest his lack of access to legal counsel. He was soon transferred back to Abepura Prison.
Amnesty International issued another alert on Karma's behalf in April 2012, when the organization alleged that prison officials were refusing to provide him medical treatment for a possible tumor. He received treatment in September of that year.