Viljoen was testifying before a seven-member panel of the Truth and Reconciliation Commission chaired by chairman Archbishop Desmond Tutu at a special hearing in Cape Town's Good Hope Centre.
A handful of spectators listened to his presentation, which is the first of a series of submissions by political parties this week.
"I still maintain it is unfair that the operators be exposed as the chief perpetrators of atrocities and violence in general when the politicians and strategy managers hide behind their status and positions," Viljoen said.
The masterminds of the conflict "more than anybody else" should be made accountable for their schemes even if it embarrassed their political parties.
In his 43-page submission, Viljoen repeatedly emphasised the need for reconciliation and nation-building but warned that the participation of "ethnic Afrikaners" in the process was threatened by the government's stance on amnesty.
In presenting a historical overview of the apartheid conflict from the ethnic Afrikaner's viewpoint, Viljoen said political parties' submissions to the Truth Commission should not attempt to find excuses for the wrongs of the past.
"Our presentations should certainly not degenerate into an effort to score political points for political parties for that may result in further polarisation rather than in reconciliation."
Viljoen said the cut-off date of December 6 1993 for offences for which amnesty can be sought excluded Afrikaners involved in politically motivated acts of violence after that date.
"Already prosecutions are on course and some of our people have already been jailed for offences of a political nature which cannot even be remotely compared with offences committed by other South Africans for which they are eligible for amnesty."
If nothing was done to address the amnesty issue, the FF would have to take a "hard look" at what options were left for ethnic Afrikaners and what role they could play in the new political situation.
"I will certainly have to seriously reconsider my position as a leader that has given strategic guidance towards reconciliatory politics to the people who put faith in me.
"The present situation is unacceptable and certainly not helpful to the commission in its work."
The African Christian Democratic Party's Kenneth Meshoe is to make a presentation to the commission later on Monday.
The National Party and African National Congress will make their submissions on Wednesday and Thursday respectively.