The city government said in a statement over the weekend that local police did not pick the men up and are not holding them.
At the center of the controversy is Ciudad Juarez's new police chief, Julian Leyzaola, who was dogged by allegations that he inflicted or condoned torture during his previous tenure as top cop in another border city, Tijuana.
Government human rights inspector Gustavo de la Rosa said witnesses reported that the Ciudad Juarez men were last seen March 26, when they were picked up by patrol vehicles with decals matching those used by Leyzaola's security detail.
"We have no proof that it was them (the security detail), but there must be an investigation into who was driving those vehicles, if it was not them," de la Rosa said.
The city government said it would cooperate with any investigation by the appropriate authorities. In such cases, the responsibility for investigating falls to state prosecutors.
Armida Vazques, sister of two of the missing men, said her brothers were picked up outside a street market for no apparent cause.
"The only thing we want is for them to hand them over, we won't press charges ... but we want them to returned," said Vazques.
Leyzaola took over the top police job in Ciudad Juarez on March 10. The city of 1.3 million residents across the Rio Grande from El Paso, Texas, registered more than 3,000 homicides last year amid the nation's soaring drug violence.
Leyzaola, 50, a retired army lieutenant colonel, took on drug traffickers in a close alliance with the army during his tenure as Tijuana's top cop from December 2008 to November 2010.
He was dogged by allegations that he inflicted or condoned torture. Several police officers who were charged in early 2009 with helping drug traffickers alleged Leyzaola or other officers dropped them off at a military base where they were beaten, nearly asphyxiated or forced to endure electric shocks to their genitals.
Leyzaola denied the allegations and called them part of a campaign to smear him.
The Washington-based group Human Rights Watch called for an investigation into the disappearances in Ciudad Juarez.
"Strong evidence of police involvement in the disappearances, and the lackluster investigation by state officials cast serious doubt on the ability of local authorities to investigate this crime," said Jose Miguel Vivanco, the Americas director for Human Rights Watch.