The world's number three platinum firm attributed the sharp drop in attendance to intimidation, after a high of 57 percent of workers reported for duty at the weekend.
Around 600 strikers gathered in an open space, just metres (yards) from where police shot dead 34 of their colleagues on August 16. Many more were streaming in from different directions.
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Police in armoured trucks kept a close watch over the crowd.
Earlier, dozens of other workers reported for duty more than two weeks into a wildcat strike that has claimed a total of 44 lives.
"Preliminary figures are 13 percent average attendance across all shafts this morning," said Lonmin in a statement.
"There have been incidents of intimidation towards bus drivers overnight as well as intimidation of... workers this morning, preventing them from coming to work."
Those who returned to work faced veiled threats from their colleagues who were still on strike.
"We are aware that some people have gone back to work, we have noted that behaviour, and we need to come up with a plan to deal with them," said Alfonso Mofokeng, a miner from Lesotho.
"By going to work they are say the murder that happened here was in vain, and they are fine with it," he said.
Lonmin said it was hoping most of its 28,000 workers would clock in, after promising signs at the weekend that the stand-off -- sparked by demands from rock drill operators for a 300-percent pay rise -- may be winding down.
Lonmin said it was due to meet for a fresh round of talks on Monday with representatives of the striking workers.
"The objective of these meetings is to achieve cessation of the violence and a return to work in a safe and secure environment," it said.
