A Mexican government spokesman insisted his country's institutions were strong enough to resist the increasing violence being perpetrated by the cartels.
More than 28,000 people have been killed since President Felipe Calderon launched a crackdown on drugs trafficking on taking office in 2006.
Mrs Clinton pledged US support for the operation but warned of the danger of the cartels.
'These drug cartels are showing more and more indices of insurgencies,' Mrs Clinton said.
'It's looking more and more like Colombia looked 20 years ago, when the narcotraffickers controlled certain parts of the country.'
Mrs Clinton told the Council on Foreign Relations that for stability, Mexico needs a 'combination of improved institutional capacity... married to political will to prevent this from spreading.'
Mexican officials were swift to downplay Mrs Clinton's comparison with Colombia.
'We don't share this opinion. There are very significant differences between what Colombia faced and what Mexico is facing," Mexico's national security spokesman Alejandro Poire said.
Mr Poire said that almost 40% of Colombia was once controlled by insurgents and that Mexico had not fallen to the same levels of political infiltration by drug traffickers.
Maybe 'the criminal phenomenon in Colombia and Mexico are alike in that both feed off the enormous demand for drugs from the United States,' Mr Poire retorted.
