Without elaborating, Michael Flynn told White House reporters: "As of today, we are officially putting Iran on notice."
Washington earlier declared the test to be "absolutely unacceptable".
Iran confirmed on Wednesday it had tested a missile over the weekend, but denied violating a UN Security Council resolution.
Mr Flynn did not provide any further details of what actions the US may be planning in response to the test, which Pentagon officials say failed upon re-entry into the earth's atmosphere.