The Sea Consortium (Private) Limited made the token payment in "good faith" as it did not have the financial capacity to fully cover the damages.
A petitioner who brought action against the MV X-Press Pearl, which sank off Colombo Port in June 2021, said he had been officially informed of the payment.
"I was given a copy of the affidavit of Sea Consortium (to the court) after it paid 300 million rupees ($1 million) to the Treasury," environmental activist Hemantha Withanage told AFP.
"They have done this because the court held them responsible for any non-compliance by the Singapore owners."
The move came as the owners of the X-Press Pearl told AFP in Singapore that they would refuse to pay the massive damages.
In an exclusive interview, X-Press Feeders chief executive Shmuel Yoskovitz said he believed any such payment would have wide-ranging implications for global shipping and "set a dangerous precedent".
The fire, which burned for nearly two weeks before destroying the vessel, was believed to have been caused by a nitric acid leak.
Its cargo included 81 containers of hazardous goods, such as acids and lead ingots, and hundreds of tonnes of microplastic pellets known as nurdles.
The ship had been refused permission by ports in Qatar and India to offload the leaking nitric acid before entering Sri Lankan waters.
Microplastics from the ship inundated an 80-kilometre (50-mile) stretch of beach along Sri Lanka's western coast, forcing a months-long ban on fishing.
The company had been ordered to pay the first instalment of $250 million by Tuesday and warned that further payments could follow at the court's direction.
Yoskovitz rejected the open-ended nature of the penalty.
"We are not paying because the whole basis of maritime trade rests on the limitation of liability. This judgment undermines that principle," he said.
Sri Lanka's government said it would consult its chief prosecutor on what action could be taken.
Yoskovitz said X-Press Feeders had already spent $170 million to remove the wreck, clean the seabed and beaches, and compensate affected fishermen.
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