MEXICO CITY (Reuters) - Conditions have worsened in Mexico's dangerous and overcrowded prisons, with many of them falling increasingly under control of inmates, Mexico's National Human Rights Commission (CNDH) said on Friday.

The latest annual report by the CNDH showed that the state of Mexican prisons deteriorated in 2013 compared with the previous two years, a spokesman for the commission said.

Mexican President Enrique Pena Nieto pledged to clean up the penal system when he took office two years ago, but the report found that there was a "growing system of self-government" in most of the prisons that the CNDH visited.

The commission surveyed 152 prisons containing about 88 percent of the prison population as of January 2013.

The report found that the system suffered from overcrowding and a shortage of food for inmates and that it failed to properly separate the accused from the convicted. In some cases, prisoners were found to control areas of the penal system with lock and key.

There were also not enough guards, meaning that prisoners rarely left their cells, the report found.

(Reporting by Joanna Zuckerman Bernstein; Editing by Leslie Adler)