Police told Reuters two policemen died after a machete attack by a mob near the mine. Another officer was badly injured and police in turn shot dead three protestors.
"We came under attack. The suspects took our weapons. A shootout ensued and during that incident three suspects were fatally injured," spokesman Lindela Mashigo told Reuters.
Lonmin said the situation remained "volatile" at its Western Platinum mine, 100 km northwest of Johannesburg. The plant was operating at reduced capacity and was under heavy police guard.
"We are expecting the situation to return to calm given the level of security on site," executive vice president Barnard Mokwena said.
The mine is part of Lonmin's Marikana operations, which produced 1.3 million ounces of platinum group metals in 2011. Company officials could not say how much production had been lost but they are expected to update the market later this week.
In London, Lonmin shares were down more than 1.5%.
The clashes involve a struggle for membership between the dominant National Union of Mineworkers (NUM) and the upstart Association of Mineworkers and Construction Union (AMCU).
At least three people were killed in a similar round of violence in January that led to a six-week closure of the world's largest platinum mine, run by Impala Platinum Holdings Limited [JSE:IMP].
The whole platinum sector is grappling with declining world prices for the precious metal and a surge in union militancy in South Africa, home to 80% of known reserves.
Aquarius Platinum Limited [JSE:AQP] briefly shut one of its shafts this month after an attack by unidentified assailants that left three dead and at least 20 injured.
The latest round of blood-letting is the worst yet. Two security guards were hacked to death on Sunday, while NUM said one of its members was killed late on Sunday after being ambushed while trying to report for duty.
Lonmin said a fourth employee had been found dead with several gunshot wounds.
The trouble began on Friday with an illegal strike by 3 000 rock drill operators at Western Platinum mine, echoing previous incidents when AMCU has tried to recruit NUM members.
January's stoppage at Implats also started with an illegal strike by rock drillers.
NUM and Lonmin officials told Reuters workers who wanted to report for duty were being intimidated. AMCU has faced the same allegations elsewhere but has always denied them.
General Secretary Jeff Mphahlehle told Reuters he was to have an emergency meeting with Lonmin management on Monday and said members of his union had also been attacked.
The AMCU/NUM rivalry, which has already caused friction at Lonmin's Karee mine, has now spread to other shafts at a time when the company is cutting back on investment plans in the face of weak demand and shrinking margins.
The challenge to the dominance of the 300 000-strong NUM also has political ramifications given its role as a key support base for the ruling African National Congress.