Biosecurity protocol refers to several politically-controversial attempts to unify global biosecurity measures and responses, in a similar manner to a biosafety protocol. Although some propose a "Biosecurity Protocol" to extend the Biosafety Protocol to organisms considered weapons (already controlled by UN arms proliferation treaties ), others argue this is an inappropriate response to military threats, and argue for a broad biodefense instead.

As of 2002, the latter view was prevalent in military and scientific circles, the former in NGOs, some UN agencies, and Green Parties. Most cooperation was restricted to attempts to define "biosecurity" itself.

A major issue is whether to accept the Precautionary Principle, or by extension, any restrictions on militarily-useful research by major powers. Compromises, e.g. the 2002 US government request to scientists to delete procedural details of experiments on dangerous organisms, are strongly resisted by most American scientists. Extreme positions, e.g. Bill Joy's argument for relenquishment of nanotechnology and artificial intelligence, are considered a legitimate part of the debate, but have yet to achieve any serious political support, even among Green Parties.

Whether these negotiations and compromises will yield a comprehensive biosecurity protocol is doubtful. It seems that basic political differences drive the debate which are unlikely to easily resolve, and that military alliances will influence tax, trade, and tariff systems and import/export restrictions more than any diplomatic or scientific protocol.