Johannesburg - Sixteen Engen service stations have run out of fuel in Johannesburg, the refinery said on Wednesday.
Two had run dry in Pretoria and one in Durban, said spokesperson Tania Landsberg.
"There have been no reports from Cape Town, but we are keeping a close eye on the situation."
"Gauteng is the hotspot. Three of the depots can't release oil tankers because truck drivers are on strike, and there has been a bit of intimidation," she said.
Safety of non-strikers was a concern.
"There are people picketing outside the gates of the depots and the most important aspect for us is ensuring the safety of our workers."
The depots affected were Langlaagte, Alrode, and Waltloo.
Landsberg said although contingency plans were in place across the country, there would be challenges.
Several attempts to reach Shell SA Refining spokesperson Dennis Matsane and BP Southern Africa spokesperson Glenda Zvenyika were unsuccessful.
On Tuesday, Zvenyika said fuel deliveries were increased before the strike to ensure all its petrol stations were topped up.
Sasol spokesperson Nothemba Noruwana said contingency plans were in place, and that major complexes in Secunda and Sasolburg were operating with minimal disruptions.
The Chemical, Energy, Paper, Printing, Wood, and Allied Workers Union (Ceppwawu) rejected claims of intimidation made by Engen.
"They want to discredit our strike and run away from the fact that the strike has had an impact on employers and they want to underplay that," said union coordinator John Appolis.
"Our members are on strike and that is why they can't deliver fuel. It's not because of intimidation."
He said the strike by fuel workers had been peaceful.
"Instead of making wild accusations, the employers must make a decent wage offer so that this dispute can end."
There had been no response to the memorandum workers had handed over to employers on Tuesday, said Appolis.
The Fuel Retailers' Association said most service stations were receiving fuel deliveries despite the countrywide strike.
About 70 000 fuel workers from Ceppwawu, the Allied Workers Union, and the General Industries Workers Union of SA downed tools on Monday, demanding a minimum salary of R6 000 a month and a 40-hour working week.