"All indications are that it was sabotage... the concern is that striking workers are responsible for this," said United Transport and Allied Trade Union (Utatu) general secretary Chris de Vos.
"The railway line had been fiddled with... three locomotives and four diesel tankers derailed."
The railway plates had been loosened, causing the train to derail just outside Durban in the early hours of Wednesday morning.
Nobody was injured in the derailment.
'Things could get ugly'
Asked if commuters needed to be concerned about possible petrol shortages due to the strike, De Vos replied: "Things could get ugly. The corridor between Johannesburg and Durban has now been closed...
"We [Utatu] have the biggest majority at pipelines," he added.
De Vos also said 18 locomotives were damaged in the strike on Tuesday.
This happened in Ermelo and Durban, when rocks were thrown at locomotives and some locomotives were set alight.
Transnet's spokespeople were not immediately reachable on Wednesday morning to confirm the reports.
Utatu on Wednesday joined the SA Trade and Allied Workers Union (Satawu) whose members had been striking since Monday.
Wage demands
Both unions rejected a Transnet wage increase of 11%, demanding 15%.
"The last time we spoke to Transnet was yesterday [Tuesday] afternoon when they told us to call them when we want to sign.
"We replied that they must call us when they can improve the offer," said De Vos.
Transnet employs nearly 54 000 people and Satawu represents 39% and Utatu 45% of these workers.
An estimated 15% of workers were not striking.
Transnet obtained a court interdict on Tuesday to prevent striking workers from "unlawfully interfering with business or activities of Transnet".
Thirteen people were arrested for public violence and intimidation during the Satawu workers' strike in Durban on Monday.