Officials said they discovered the damage and apparent vandalism on Tuesday during a routine check on the site, according to the Catalan Institute of Palaeontology (ICP).
ICP director Salvador Moyà compared the act to the destruction of cultural symbols performed recently by Islamic State fighters.
"It is totally unacceptable," said Moyà in a statement. "Paleontological heritage is cultural heritage and should be protected with the same intensity as archaeological heritage."
This is not the first time that the site was tampered with. In 2013, a man stole a fossil from the site, but later returned it. A court fined the man €90 for the theft.
The culprit of the most recent damage is not yet known, though officials told El País that they did not believe it was connected to the previous crime. An investigation is now underway after the ICP filed a complaint with Catalan's Department of Culture.
Dinosaur eggs are scarcely found in Europe, but Coll de Nargó is home to some of the biggest discoveries of dinosaur eggs on the continent. Scientists found four different species of dinosaur eggs and an abundance of eggshells and nests on the site in 2013.