The extreme weather conditions and the passage of time eventually cracked and eroded the material sealing the testing tunnels. By 2004, scavengers looking for scrap metal to sell had broken into some of them. Reports of the looting alarmed U.S. officials, who feared that fissile material could be at risk. The U.S. government encouraged and aided the Kazakh government to improve security at the site until more permanent measures could be implemented. Astana declared an exclusion zone, where a ban on trespassing was strictly enforced, and mounted patrols to guard the tunnels and the surrounding area.

Next, nuclear weapons scientists who once sat on opposite sides of the Iron Curtain determined how best to secure the material. They decided to fill the test chambers with a specialized grout, which bonds chemically with fissile material to render it useless for weaponization. In some tunnels, it would be necessary to mine horizontally to reach the test chamber where the nuclear experiments took place.

It was hazardous work: The old tunnels were partially collapsed and dangerous to enter. At other sites, the cement could be pumped from above after drilling into the test chambers. In every case, once the work was done, removing the cement would require a major mining operation that required specialized equipment and was beyond the capability of scavengers or would-be terrorists. Because fissile material was involved, the International Atomic Energy Agency (IAEA) was also informed of the project.