 The number of people trying to use the metro has almost doubled
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Chilean President Michelle Bachelet has sacked four ministers, as polls suggest falling support for her government.
The last few months have seen protests in the capital, Santiago, over the introduction of a new transport system.
In a national TV address, Ms Bachelet said her government owed an apology to Santiago's residents, especially the poor, for the chaos they have faced.
It is the second big cabinet reshuffle since she took office in 2006. The first one followed student protests.
Increased strain
Speaking on Monday evening, Ms Bachelet said her government was beginning a new era in which mistakes would no longer be accepted.
Transport Minister Sergio Espejo - one of those removed from his post on Monday - had been the focus of criticism since the Transantiago transport system was introduced on 10 February.
With the Transantiago, large areas of Santiago - a city of about 6m inhabitants - were left almost devoid of public transportation, forcing people to walk long distances to catch a reduced number of buses.
The system came under more strain with the start of the school year at the beginning of March.
The capital's metro system has been unable to cope with the large numbers of commuters, with reports of people fighting to get on overcrowded trains.
Emergency rooms
The number of passengers trying to use the underground is said to have almost doubled, with some 2.2m users in a week.
One person is reported to have died from a heart attack as a result of the crush, another died after fainting from lack of oxygen.
The authorities have set up emergency rooms to deal with the increased numbers of cases of fainting due to the lack of oxygen and higher temperatures.
The transport problems have sparked frequent protests in Santiago's poorer neighbourhoods, where roads have been blocked with barricades.
Ms Bachelet - whose popularity rating is said to have fallen to about 47% - also replaced the justice minister, the defence minister and her chief of staff.
Have you been affected by the travel problems in Santiago? Send us your comments and experiences using the form below. If you have any pictures of your commute you can send them to yourpics@bbc.co.uk.
