The eight week old terrier crosses were found by revenue officers, and were destined for the UK.
The DSPCA says they had no access to water and would have remained in the sealed boot for the entire journey on the ferry.
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The owner, who could not provide any vaccination certs or the relevant paperwork required to transport dogs out of Ireland, surrendered the puppies at the port.
The DSPCA says they will be placed on foster care until they are ready to be rehomed.