The alleged harassment took place over an extended period of time and involved the Swedish officer's commanding officer.
"The commander behaved in a totally unacceptable manner," Brigadier General Anders Brännström, the Swedish Army's Chief of Staff, told the TT news agency. "He has belittled her, discriminated against her, and insinuated that she has had sexual contacts with her colleagues."
It was at a party about a month ago that things really got out of hand.
"It degenerated to sexual harassment. He was lewd and demeaning to her," said Brännström.
The Swedish officer then reported the incident to another one of her superiors, and the offending commander was removed from service. The victim was then sent home to Sweden, at which point the alleged offender was promptly allowed to return to service, a move that left Brännström fuming.
"If he was my soldier he would have been sent home on the first flight," he said.
The mission commander has since his contacted EU military leadership and his counterpart in the country from which the suspected commander hails.
"The EU has decided to investigate the incident, which is positive," said Brännström, who hopes the female officer will soon be able to return to the training field.
About ten percent of Swedish soldiers serving overseas are women, but Brännström said harassment is a rare exception, not the norm.
"Sexual harassment and violations aren’t any sort of pattern," he told TT. "But there are deviations, people who do offend, and in such cases they must be removed from the operation."