Chilean researchers contend that the grave site was plundered and the mummified skeleton was stolen, violating the country’s laws.

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Days after researchers announced that a tiny mummy once rumored to be an alien was actually a human infant, Chilean scientists condemned the new study as unethical and their government began an investigation into grave robbing.

The Chilean National Monuments Council, a government agency, said in an email Tuesday that it had initiated an inquiry into whether the little girl’s remains were illegally exhumed in 2003 and smuggled out of the country. The council has turned over its records to the Public Ministry of Chile in response to the outcry from Chilean researchers. They contend the grave site was plundered and the mummified skeleton was stolen, violating the country’s laws.

“It’s offensive for the girl, for her family, and for the heritage of Chile,” said Francisca Santana-Sagredo, a biological anthropologist at the University of Antofagasta in Chile and the University of Oxford in England.

In a telephone interview, two authors of the new study, Dr. Garry P. Nolan, an immunologist at Stanford University, and Atul Butte of the University of California, San Francisco, defended the ethics of their research.

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“We had no involvement or knowledge of how the skeleton was originally obtained nor how it was sold or exported to Spain,” Butte said. “We had no reason to suspect in this case that this sample was illegally obtained.” He noted that there were reports about the remains on Chilean television for 15 years without the government investigating the case.

Those reports, from the early 2000s, indicate that a man named Oscar Muñoz discovered the 6-inch-long mummy next to an abandoned church in a ghost town called La Noria. The body was remarkable not just for its size, but also for its abnormalities, including an elongated skull that ended in a point, giant eye sockets and bones that were as mature as those of a 6-year-old.

Rumors spread that Muñoz had found an alien. It gained the nickname “Ata,” for the Atacama Desert in Chile where the remains supposedly came from. (In fact, La Noria is more than 450 miles north of the desert.)

Eventually Ata ended up in the private collection in Barcelona of Ramón Navia-Osorio, who did not immediately respond to an email query about whether he had legally obtained Ata’s remains.

In 2012, the producers of a documentary claiming to have evidence of UFOs got access to Ata’s skeleton.

When Nolan learned of their efforts, he offered to examine samples sent to him for DNA.

Working with a team of researchers from both Stanford University in California and the University of California, San Francisco, Nolan reconstructed Ata’s entire genome. Far from being an alien, they concluded, Ata was a Chilean girl who was probably stillborn and suffered from previously unknown bone disorders.

Publication of the study in the journal Genome Research enraged some researchers in Chile, where the looting and sale of artifacts and mummies have long been a concern.

Like many other countries, Chile now has laws that make such exhumations and smuggling illegal, punishable by fines and prison sentences. But it can be hard to stop treasure hunters from plundering remote sites.

On Sunday, Cristina Dorado, a biologist at the University of Antofagasta, called the study an “outrage” in a commentary on Etilmercurio, an online science publication in Chile. “If samples are obtained unethically, any resulting science is not ethical,” she wrote.

Chilean scientific societies also condemned the study. “Could you imagine the same study carried out using the corpse of someone’s miscarried baby in Europe or America?” the Chilean Society of Biological Anthropology asked in a statement released Wednesday.

The society, along with a number of Chilean researchers, also co-signed a letter that was on Wednesday to Genome Research, the journal where the Ata study was published. “The scientific community in Chile is deeply upset and concerned about this situation,” they wrote.

Hilary Sussman, editor of Genome Research, said the journal “is paying close attention” to the issue of studying DNA from human remains, and “will return to it in future issues of the journal.”