The army and related agencies use a large number of animals in harmful experiments. In Israel, no official statistics are available about the number of animals used by them, but according to estimates, tens of thousands of animals are used annually by such agencies.

Little is known about what actually happens to animals in military laboratories. The Institute of Biological Research in Ness Ziona is under the direct responsibility of the Prime Minister's office. According to foreign publications, this research institute conducts offensive and defensive weapons research on live animals. It appears that both chemical and biological warfare agents are tested there on a variety of animals. The Ness Ziona institute is one of Israel's largest users of non-human primates. In 2001, for example, the Institute of Biological Research imported 32 rhesus monkeys from the U.S.

The Israeli army also uses animals for various other purposes. For example, in the past, use of dogs to test ballistics was exposed. The army uses dogs for ATLS courses (see Educational Use), despite the existence of alternatives.

Under Israeli law, military experimentation is subject to even less supervision than other types of animal research. Clause 20 of the Animal Welfare (Animal Experimentation) Law of 1994 allows the internal use committee in the army to deviate from the rules and regulations issued under the Law, if this is "necessary for national security." Since no representatives of animal protection organizations sit on the army committee, animal experimentation by the army and related agencies is veiled in secrecy and does not stand up even to minimal standards of public accountability — despite the fact that all such experimentation is paid for by public tax money.

However, in September 2013,  the only military medical school in the U.S. announced that it no longer uses live animals in its training programs. The school says it now uses human-based simulators to teach surgical skills and physiology.