Experts have sent seven reports over the orphanage to the child protection authorities, alleging that caretakers at the facility force-fed children, swore at them and pulled their hair, reported.
More than a thousand children live in Latvia's orphanages.
Experts were sent to review all of them as part of a deinstitutionalization project that would halve the number of children staying in such institutions by 2024 and improve existing facilities.
At Jelgava, a team of seven experts witnessed distressing acts against defenseless young people.
"What I experienced was hell ... adults and support personnel no longer control neither their emotions, nor their actions," said psychologist Andrija Likova.
"There's a constant background of emotional violence with threats and overstepping physical boundaries. The most popular threat [for instilling discipline] is taking [children] to psychiatric facilities," said Likova.
In addition, children are routinely sent to boarding schools in distant regions while the state still pays the support money, meaning there might be pecuniary incentives for the orphanage to send them away.
Another episode from the reports describes a child kept under lock and key in Jelgava. A caretaker was unable to describe why the minor had been locked up. He had bruises on his hands and legs and claimed he was beaten up by a caretaker at the Adamova boarding school in Latgale.
Meanwhile Maija Neilande, the head of Jelgava Orphanage, claims that telling children they might be sent to psychiatric hospitals serves an informative purpose.
"Children have to do these things and do something for the sake of their health. It's not threatening. It's informing the children," she said.
A child staying at the orphanage describes Neilande as abusing a pregnant peer of hers.
"The manager Maija Neilande is awful. She hates girls. She hits them and pulls their hair. One girl was expecting a little one, and the manager called her names, pulled her hair when passing by, and called her stupid."
Other gruesome testimonies by children describe force-feeding and verbal abuse.
Likova further claimed that personnel at the orphanage was violent against children even as she was present. She described a caretaker pulling a child by her hair and stopping only when Likova intervened.
Confronted with excerpts from the report, Neilande denied any wrongdoing on her subordinates' part and insisted she doesn't want to step down from managing the orphanage.
People who formerly stayed at the institution, lead by Neilande for 23 years, contacted Latvian Radio, claiming that she instilled fear not only in the children but even her colleagues.
There are 44 employees at the Jelgava City Orphanage. Three have been suspended during the investigation.
Latvia's State Inspectorate for Protection of Children's Rights has found that the orphanage sends children to boarding schools without due cause, is little interested in their success at school and uses unacceptable methods for disciplining children.
The inspectorate will be presenting the findings to Neilande and also possibly call for the municipality to review her suitability for the post.
Meanwhile Welfare Minister Jānis Reirs said that municipalities are largely responsible for the situation in each institution.
"There are great institutions where children are directed and returned to normal life. And then we have cases like these. But I wouldn't agree that this is a systematic situation," he said.