The three men were kidnapped from a Baghdad apartment known to be a brothel, an Iraqi security official with knowledge of the investigation told CNN.
Investigators were trying to determine whether the men had been lured to the brothel or the kidnapping was opportunistic, the Iraqi official said.
The men were identified as two Iraqi-Americans and one Egyptian-American.
The missing men work for a security service company called Sallyport, the Iraqi official said. However, a spokesman for Michael Baker International, Sallyport's parent company, said the report was false.
"(The missing men are) not employees of Sallyport or any other subsidiary," Brian Peiritsch said.
Gunmen grabbed the men at an apartment in Baghdad's southeastern Dora neighborhood late Friday afternoon.
A security operation was underway in the al-Saha part of the Dora neighborhood, an Iraqi intelligence official with Baghdad operations command told CNN on Monday.
The contractors were taken away in a vehicle convoy, said the source, who talked to CNN on condition of anonymity, as he is not authorized to speak to the media.
Baghdad's Dora neighborhood is a religiously mixed one, its residents consisting of Shiite, Sunni, Christian and other faiths.
The U.S. State Department said it was aware of the report that American citizens are missing in Iraq
"We are working with the full cooperation of the Iraqi authorities to locate and recover the individuals," spokesman John Kirby said in a statement.