Gabriel Mocho Rodriguez of the International Transport Federation said the complaint was lodged today with the International Labour Organization (ILO).
The union body wants the UN labour agency to condemn the wholly state-owned airline for violating global rules on workers' rights, as well as domestic regulations.
"We're urging the ILO to make the recommendations necessary to bring the Qatar government into compliance with its international commitments as soon as possible and end the disgraceful measures," Rodriguez said.
In April, the ILO urged Qatar to remove a host of restrictions on forming unions and striking, and to protect workers from discrimination.
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Beyond the dearth of union rights, Rodriguez said, Qatar Airways staff must live in company compounds, under surveillance, with curfews.
They are banned from marrying during their first five years at the company and must obtain its permission thereafter.
Staff face regular medical checks, including AIDS tests.
"Any infringement of the draconian regulations imposed on them is likely to result in sacking and deportation," Rodriguez said on the sidelines of the ILO's annual congress.
He said the rules were rarely made clear to would-be staff before they had actually joined, and that they were bound by gagging clauses thereafter.
"Compared to the one-and-a-half million migrant workers in Qatar, there are a small number of aviation workers, around 20,000. They might have better salaries, they might have neat and tidy uniforms, but that does not mean they don't suffer," he added.
Over 90 per cent of its staff is foreign, reflecting the overall proportion of migrant workers in the Qatari economy.