And President Bill Clinton has to decide, possibly as early as the summer, whether to go ahead with initial construction of the missile defence system, probably at a base in Alaska.
Click here for a diagram of failed test
A further test is tentatively scheduled for April or May before Mr Clinton makes his decision.
In a similar test carried out last October the interceptor did find its target but the Pentagon has revealed that there were also some technical problems.
Russian fears
The test programme has international implications and was being watched closely by governments as well as contractors, including Boeing, integrator of the proposed national missile defence system, and Raytheon, which builds the 55kg (121lb) weapon.
Although it would not be capable of stopping a major missile attack on the US, the system could prevent a ballistic missile, launched accidentally from countries such as Russia or China, from hitting its target.
Both those countries say that such a project would simply spark another arms race, leading to the production of even larger missiles.
Russia has warned that a US national missile defence system would violate the 1972 anti-ballistic missile treaty.
Moscow has refused a US request to modify the treaty to allow the system and cautioned that a go-ahead by Washington could threaten current nuclear arms reduction agreements.
The White House and Pentagon have said it would be a very modest successor to former President Ronald Reagan's "Star Wars" missile defence plan.
They say it would protect US cities from limited attack from countries, such as North Korea and Iraq - regarded by Washington as "rogue states" - but would not neutralise Russia's massive nuclear arsenal.