The biotope was created in 1987 by a ruling crafted by the Petén Land Commission (CTP, 1987). In 1989, the Law of Protected Areas conferred its official status (Decree 4-89), and in 1990, the Declaration of Maya Biosphere Reserve established the area as a core zone (Decree 5-90).
The biotope is run by the Center for Conservationist Studies (CECON) of the Faculty of Chemical & Pharmaceutical Sciences of San Carlos de Guatemala University (USAC), an autonomous governmental entity. Although the National Council of Protected Areas (CONAP) is not directly in charge, it approves operating plans and master plans. The Institute of Anthropology & History (IDAEH) is responsible for the archaeological sites.
A master plan was drafted for the protected area in 1999, to be applied to the period from 2000-2004. The plan is complex and complete, and is divided into three programs: environmental management, public use, and administration. Each of the programs is subdivided into subprograms, making 13. The subprograms include a precise list of a series of activities to be carried out in the biotope. The master plan is to be renewed every five years, in addition to annual operating plans. Despite this, most of the programs are not being carried out, and activities are currently limited to maintenance and vigilance.
The master plan establishes seven different zones within the protected area:
1. Extensive Use Zone: The goal of the Extensive Use Zone is to maintain the area as pristine as possible, albeit permitting extraction of forest products and access to vehicles of those involved in harvesting. Although the area has not been measured, it is one of the largest zones in the biotope, including the entire southern section and part of the north side of the biotope.
2. Intensive Use Zone: The goal of this zone is to facilitate internal transport, education, recreation, and interpretation. The area is located along the road that crosses the biotope from the southeast to the north, covering a 100-meter wide strip around it.
3. Transitory Agricultural Use Zone: This zone is the most heavily-transited area in the biotope. The aim of this area is to control the expansion of farming in the area and prevent agriculture from causing a negative impact on the rest of the protected area. The ultimate goal is to help the area recover its original ecosystems. It is located in the western-southwestern corner of the biotope.
4. Archaeological Zone: This area is home to the biotope's main archaeological sites. The goal of this zone is to protect the archeological ruins and their natural surroundings. This zone is confined to El Zotz and El Diablo sites.
5. Ecological Recovery Zone: This zone covers portions of the biotope where the habitat had been severely altered in the past but has been left to regenerate. The goal of this zone is to halt further degradation of the ecosystem and return the area to its natural state (as much as possible). The zone does not form a continuous area, but covers sites that were once populated, the main ones being those on the western edges of the biotope and along the main road.
6. Primitive Zone: The primitive zone includes the least-impacted portions of the biotope. The aim of this zone is to preserve the natural environment and facilitate scientific studies, education, and low impact recreation. It lies in the eastern section of the biotope, bordering Tikal to the east and the Maya Biosphere Reserve's Multiple Use Zone to the north, and the Maya Biosphere Reserve's Buffer Zone for extensive use to the south.
7. Buffer Zone: This zone is a 1 km wide strip surrounding the biotope to the north, south and west. The objective is to facilitate monitoring of the borders of the protected area and prevent unauthorized persons from entering.
The biotope has a total of 11 employees. CECON provides eight employees; four park wardens, three maintenance staff, and one administrator that is responsible for all four biotopes run by the CECON's Petén center, which means he does not work full-time in the area. Employees work two shifts -22 days on, eight off. This means that there are only three or four people in the field at any given time. Patrolling is therefore extremely limited. IDAEH employs three guards for the archaeological sites of El Zotz and El Diablo. These employees also work 22-day shifts, leaving at times just a single guard in the field. There is another employee, but he only conducts site visits to El Zotz several times a year. Both groups have a series of installations in good condition. These installations are located several hundred meters apart. Because of the distance, the groups cannot make visual contact and therefore have difficulty communicating. Workers from both institutions lack equipment, and do not carry weapons. In addition, those people engaged in illegal activities do not respect their authority. The borders of the biotope are defined and marked by signposts and gaps cut into the vegetation. However, the borders are not obvious because inconsistent maintenance and lack of signposting.
The budget for El Zotz is difficult to calculate with precision; it comes from a larger budget covering the four biotopes managed by CECON. In 1991, the budget for San Miguel la Palotada (El Zotz) and Biotope Laguna del Tigre totaled US$93.000 (CONAP 1999c), mostly provided by a program called "Mayarema." The agreement signed between CONAP and CECON to carry out that program expired in 1999. In 2002, the University of San Carlos de Guatemala (USAC) provided a $6,400 grant to finance infrastructure in the protected area. Today the regular budget totals US$15,000 and covers workers' salaries. Minor expenses, such as fuel, are covered by a CECON managed fund financed by entrance fees to Biotope Cerro Cahuí, where the institution is headquartered in Petén.