Marcelo Ebrard, the mayor of Mexico City, said the city would create a new police investigative agency to replace its old, reportedly corrupt, detectives unit.
Mexico City detectives are suspected of having participated in the abduction and killing of 14-year-old Fernando Marti, the son of a prominent businessman.
His body, found on August 1, sparked widespread public anger.
Experts say kidnappings have not only increased but have also become more violent with the involvement of drug gangs seeking extra money to survive a government crackdown, a claim the government has denied.
Juan Camilo Mourino, the Mexican interior minister, said there was "no evidence that the increase in kidnappings is related" to the fight against drug gangs.
"On the contrary, the fight against organised crime ... has been reducing the financial and operative capacity" of criminal groups, he said.
Despite the security forces' operation launched in March, however, including the deployment of more than 36,000 soldiers across the country - the violence has continued.
In Ciudad Juarez - where about 2,500 soldiers have been deployed - 15 people died on Saturday, six on Sunday and eight on Monday in separate incidents.