It took place in three areas in Deeside on Thursday following complaints that men had been held "virtual captives" for up to three years.
North Wales Police said the conditions they were living in were "utterly appalling".
The arrested man is local to the area and will be questioned by detectives.
Another man will be "voluntarily interviewed" at a later date.
Thursday's operation is part of a wider operation which aims to tackle serious and organised crime in north Wales, with a specific focus on human exploitation.
Det Ch Insp Neil Harrison said: "As a result of this morning's operation we have safeguarded, or simply put, freed, at least three people who are now being assessed."
A firearm, stolen property and a "significant amount of unaccountable cash" were also recovered and will form part of the investigation.
Ch Supt Sasha Hatchett, who oversaw the operation, said: "It is sometimes a common misconception that modern slavery is an issue for other parts of the world.
"The reality is that human trafficking exists right here on our doorsteps in communities across north Wales."
Police have arrested a man for human trafficking offences and taken three people to a "place of safety" during a joint operation in Flintshire.