President Enrique Pena Nieto's spokesman Eduardo Sanchez told the BBC that a "crusade" was needed to "re-establish the rule of law".
The students, all trainee teachers, went missing after attending a protest in Iguala in Guerrero State.
The official explanation is that the students were murdered by a drugs gang.
The gang was said to be in collusion with the mayor of Iguala, Jose Luis Abarca, who has been arrested facing accusations that he ordered police to confront the students on the day of their disappearance on 26 September.
In the past decade, more than 100,000 people have been killed and 27,000 have disappeared in Mexico.
Thousands of people have taken part in protests over the disappearance of the students.
Mr Sanchez said the government wanted dialogue, but added that some groups had "taken advantage of the situation to provoke violent acts and that is absolutely inexcusable".
He said the government was working on reforms to re-establish the rule of law.
Mr Sanchez said: "We are aware that there is an institutional weakness in some local governments, where we need to work harder for them to uphold the rule of law, where citizens respect the authorities and the legislations."
Mexico's government has vowed to take action to restore the credibility of institutions after the disappearance of 43 students more than two months ago.