Daniel Bennett had been studying the butaan lizard for more than five years in the Philippines and was working towards a doctorate.
He had built up a large collection of faeces samples which were stored at Leeds University and then disposed of.
The university said Mr Bennett was still due to finish his PhD this year.
Unfortunately he will now have to pass his oral defense without the benefit of key visual aids for show-and-tell.
Mr Bennett said he spent seven years of painstaking work searching the rainforest to find the faeces of the large and mysterious lizard.
He said the reptile was so shy that he studied what it ate through its droppings, rather than trapping or disturbing it.
The university said: "The loss of these samples was an unfortunate mistake.
"They were thrown away in error because they were in an unmarked bag.
Leeds University has offered to compensate him 500 pounds (about $750) for his loss. Mr. Bennett thought that was crap, declined the offer, and will take the matter to court.
He may also be harbouring dark fantasies about what he would like to do with "an unmarked bag" of shit, some citronella oil and a barbecue lighter right about now.