Lonmin, grappling with soaring costs and low platinum prices, briefly shut the two shafts earlier this year when community members held protests to demand jobs.
"We are experiencing minimal challenges as some buses to our E2 and E3 shafts are running later than usual," said Lonmin spokeswoman Wendy Tlou.
"We are monitoring the situation and have added security to assist with the safe transportation of our workers."
Bapo spokesman Vladimir Mogale said the protesting workers had not been fully paid because their traditional council had not receive its five million rand (£267,690) annual economic development funds from Lonmin.
Lonmin's Tlou said only three million rand would be paid to the community in November due to financial constraints and the rest paid in 2018 as the contract requires.
A police spokeswoman said protesters blocked roads and burned tyres on Wednesday night, but the situation was "under control at the moment".
Lonmin struck a deal with the Bapo ba Mogale community which saw it get equity in the miner through an investment company set up by its traditional council and which has been given opportunities to supply services to the mines.
But the Bapo has called for Lonmin's mines to be shut by the mines ministry because it believes the firm has failed to build enough houses or employ and train enough community members.
Lonmin shares were up 3.4 percent to 68 pence at 1209 GMT, having slumped about 30 percent on Friday when the company delayed annual results.
(The story was refiled to correct the share price move in the last paragraph to 30 percent)
(Reporting by Zandi Shabalala; Editing by Veronica Brown and MarkPotter)
By Zandi Shabalala