Despite a six-year effort to build trusted computer chips for military systems, the Pentagon now manufactures in secure facilities run by American companies only about 2 percent of the more than $3.5 billion of integrated circuits bought annually for use in military gear.

That shortfall is viewed with concern by current and former United States military and intelligence agency executives who argue that the menace of so-called Trojan horses hidden in equipment circuitry is among the most severe threats the nation faces in the event of a war in which communications and weaponry rely on computer technology.

As advanced systems like aircraft, missiles and radars have become dependent on their computing capabilities, the specter of subversion causing weapons to fail in times of crisis, or secretly corrupting crucial data, has come to haunt military planners. The problem has grown more severe as most American semiconductor manufacturing plants have moved offshore.

Only one-fifth of all computer chips are now made in the United States, and just one-quarter of the chips based on the most advanced technologies are built here, I.B.M. executives say. That has led the Pentagon and the National Security Agency to expand significantly the number of American plants authorized to manufacture chips for the Pentagon’s Trusted Foundry program.