On 3 June 2006, the Coordinating Assembly held a new assembly in the Internado Nacional Barros Arana. However, speculation began to arise concerning a split between the radical and moderate groups of the Assembly, which would explain the resignation of César Valenzuela as spokesperson (he insisted that he had stepped down in order to look after his sick mother). Rumors began to spread that some of the traditional schools of Providencia and Santiago were holding parallel talks with Zilic and that one of the leaders of the Assembly, the communist spokesperson María Jesús Sanhueza, had been removed because of her extremist positions. Nevertheless, the ACES later expressed that all of these rumors were unfounded and part of a government strategy to undermine the movement.
Meanwhile, more than one hundred groups showed their support for the Monday 5 June strike, including a call from the Frente Patriótico Manuel Rodríguez to march in protest, contrary to the wishes of the student leaders who had called for peaceful demonstrations from within the schools. The call from the FPMR provoked much annoyance in the government (motivating the Minister Ricardo Lagos Weber to declare that this act was condemnable); however, the student leaders expressed that the FPMR were within their rights to demonstrate as they wished but that they should assume full responsibility for their actions.
The strike was held on Monday with the additional support of university students, high school teachers, truckers and workers amongst other unions. There was relative calm during the morning apart from a few minor isolated incidents close to the Plaza Italia by an unauthorized march and the burning of tires in the Alameda and Del Sol Highway around 7 a.m. Throughout the country, protest activity was dissimilar: while there were almost no protests in Punta Arenas, more than 140 establishments in the Bío-Bío Region, 58 in Iquique, 9 in Coihaique were occupied as well as the only school on Easter Island. Peaceful marches took place in Osorno, Puerto Montt and La Serena as well as Valparaíso where more than 12,000 people peacefully gathered.
In Santiago, the majority of the occupied schools underwent protests of a cultural natural within their premises, the largest of which took place in the Instituto Nacional and the nearby the University of Chile's main campus. Nevertheless, as the afternoon wore on, disorderly behavior and looting began to take place which led to the mobilization of the Carabineros, who later attacked the people gathered at the Instituto Nacional with tear-gas and water cannons, which according to Germán Westhoff, President of the Student Center, was a "provocation on the part of the Carabineros". In all, more than 240 people were detained during this day of mobilizations.
On June 6, the student assembly wrote a letter to the Minister of Internal Affairs informing him that they saw the creation of a presidential advisory committee -- announced by Bachelet in her speech of June 1 to discuss the long-term demands -- as a positive step, adding that it should include students, teachers, school administrators, education experts and other social stakeholders and that half of them should be determined by the student assembly. This petition was rejected by the government because it was considered excessive, explaining that the president was free to decide who should be included. On June 7, the president announced a committee of 73 members, which included six seats reserved for high school students.
According to El Mercurio, on June 7 50 schools in Santiago and 175 across the country ended the strikes and were in conditions to return to classes. According to La Tercera, the number of schools ending mobilizations was close to 500.
On June 9 the student assembly agreed to participate in the committee and put an end to strikes and school take-overs.