Reckitt Benckiser gave £38,000 to the Maritime and Coastguard Agency (MCA), £5,445 to Cornwall Council and more than £5,000 to the National Trust.
The bottles started arriving on the Lizard in Cornwall in January but were also washed up in Devon.
Agencies said the bottles posed a risk to wildlife.
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The MCA said it was thought the bottles had come from the MV Blue Ocean which lost a container holding nearly 19,000 of them near Land's End in May last year.
The compensation figures were confirmed by the agencies involved in the clean-up.
Justin Whitehouse, lead ranger for the National Trust on the Lizard said he did not believe the pollution in the sea had been serious.
"Much of the clean-up was done by volunteers which wasn't factored into the cost," he said.
"It was local people mucking in and helping out, but that's what we're good at."
No-one was available for comment from Reckitt Benckiser but in January it said: "RB has strong history of environmental performance and the protection and preservation of the environment is our top priority."
A firm has paid out nearly £50,000 to clear thousands of its bright pink Vanish plastic detergent bottles that washed up on beaches.