The violence comes amid heightened tensions after deadly strikes at the platinum mine last year.
The local shaft leader "was killed in front of the union offices," said National Union of Mineworkers (NUM) regional spokesperson Mxhasi Sithethi.
The shootings at the Marikana mine near Rustenburg, north-west of Johannesburg, follow the assassination of a leader from NUM's rival union, the Association of Mineworkers and Construction Union (Amcu), last month.
Last August, police shot dead at least 34 people in a single day at the Marikana mine.
On Monday, two unknown men approached the NUM leader at around 10am and fired at him, said Sithethi.
"There was no confrontation. Nothing," he said. "He ran back to the office. They followed him and killed him."
The victim, whose identity has not been released, suffered at least two gunshot wounds to the head. The attackers then shot the union treasurer at least six times when he confronted them, said Sithethi.
The treasurer is in a "critical condition" in hospital, according to NUM's secretary general Frans Baleni. The police weren't immediately available for comment.
On Monday, Business Day reported Lonmin had agreed to grant union threshold rights to the Amcu, shutting rival NUM out of collective bargaining.
Lonmin human resources head Abey Kgotle told Business Day that the company agreed during negotiations at the Commission for Conciliation, Mediation and Arbitration that it would set threshold rights of 35% for basic rights and 45% for collective bargaining and rights to full-time shop stewards. Rights for a majority union would stand at 50%.
A trade union would need to achieve these levels of representation in the workforce for it to enjoy the specified rights.
Amcu currently represented 70% of unskilled workers and machine operators in bargaining unit one, Business Day reported.
This meant that the NUM would not have organisational rights among the low-skilled workers.
Lonmin operations has been a battleground between Amcu and the NUM, whose members now made up only 20% of the workforce. – AFP, Sapa