After more than two years in the role of COO and director, Ben Moolman will step down on April 5, Lonmin said, without naming a successor.
The world's third largest platinum producer, which was saved from collapse in 2015 with a $400 million (326.4 million pounds) deeply discounted rights issue, reported weaker than expected production, saying that larger shafts, known as generation 2 shafts, had disappointed. Lonmin also said initiatives to improve production were taking longer than planned.
"Its not ideal that their main technical person is gone. It's another signal that Lonmin has some real problems," Peel Hunt analyst Peter Mallin-Jones said.
"They are facing challenges in managing its workforce, managing the local community and managing the age of its assets, all at a time when platinum group metal pricing is relatively low and therefore margins are very thin."
Platinum prices XPT= rose just 1 percent in 2016, failing to join the rebound in the prices of some other metals and leaving Lonmin out of the wider recovery in share prices in the mining sector that began last year.
Lonmin has also been taken to task by the South African government which threatened to take away its licence at the end of last year if it did not build the houses it had promised for its employees.
However, some analysts said Moolman's resignation was not a concern.
Momentum SP Reid Securities analyst Sibonginkosi Nkosi said Lonmin's chief executive Ben Magara was a seasoned operations manager and could handle major issues.
"I was questioning why Lonmin needed a COO when Ben Magara is an operations guy. We know that he is Mr Fix-It. That function (of COO) can easily be slotted in under Magara," Nkosi said.
Reporting by Zandi Shabalala; Editing by Greg Mahlich