The year-old reptiles, which arrived on a flight from Malaysia, had fought each other during the journey due to their cramped circumstances.
Each of the five transportation boxes used had room for four crocodiles – but 10 foot-long animals were in each one.
A Border Force spokesman said “little attention” had been paid to the crocodiles’ welfare.
One crocodile has since died.
The animals had been destined for a farm in Cambridgeshire where they were to be bred for meat but are now being cared for by officials from the Convention on International Trade in Endangered Species (CITES).
A Home Office statement said the remaining 49 crocodiles will be re-homed.
Grant Miller, head of the national Border Force CITES team at Heathrow, said; “It is just not acceptable for reptiles to be transported in this way”.
He added that they will seize anything that contravenes CITES regulations, so this should serve as a warning to those thinking about transporting wildlife in such conditions.