Human rights groups have accused Mexican authorities of using arbitrary detentions, trumped-up charges and excessive force in an attempt to quell a mass protest movement unleashed by the disappearance and presumed murder of 43 students.

The complaints centre on the indictment for attempted murder, criminal association and rioting of 11 protesters who were arrested after masked youths clashed with police in the central Zócalo square, following a huge and mostly peaceful march through the capital last Thursday.

Supporters of the 11 accused insist that they had nothing to do with the violence, alleging that several of the detainees were arrested later, during an aggressive police operation to disperse the crowd.

“There is no evidence that they did anything other than attend the march,” said Fernando Ríos of the Mexican human rights network All Rights for Everybody. “What we do know is that the police used excessive force as they cleared the Zócalo.”

Ríos said human rights groups fear the crackdown is associated with a recent statement by President Enrique Peña Nieto, who accused violent protesters of “kidnapping” the wave of indignation triggered by the disappearance of the 43 students after they were arrested by police in the southern city of Iguala.

“This is more than an attack on freedom of expression,” Ríos said. “It is an effort to discourage people from demonstrating for the truth and for justice in the face of an inoperative, ineffective state that only pretends to be acting in the case [of the students].”

The eight men and three women arrested on Thursday are now being held in high-security jails hundreds of miles from Mexico City. The detainees – most of whom are students – include a 47-year-old Chilean doctoral student, whose case has prompted demonstrations in the Chilean capital, Santiago.

In an interview on Radio Fórmula on Monday, the interior minister, Miguel Ángel Osorio, insisted that any detainees not involved in the violence “have nothing to worry about”.

He added that the police “passed from tolerance to action” in the face of violence at the march because “a majority of Mexicans are asking for a stop to this kind of behaviour”.

Videos and testimonies documenting the aggression of the police at some distance from the battles in front of the presidential palace have been widely circulated on social media.

These include the account of Layda Negrete, one of two lawyers behind a hit documentary called Presumed Guilty which exposed systematic abuses of due process in Mexico’s capital city.

After being pushed against shop fronts by riot police forcing back the mass of peaceful demonstrators, Negrete says officers shouted, “fucking bitches, is this why you wanted to come out and march?” while they attacked her and three other women with their truncheons and shields.

“It is very worrying that a march to repudiate crimes committed by police ended with more crimes committed by police,” the lawyer said.