U.S. Northern Command confirmed it was not a launch by a foreign country and said it was not a threat.
Vandenberg Air Force Base said it did launch a missile Friday night but did not have any launch Monday night.
A Vandenberg official who saw footage of the contrail said it appeared to be a missile, possibly launched from a Navy post on an island near Catalina.
The U.S. Navy said it did not test fire a missile Monday. The U.S. Air Force also said they did not fire off a missile.
The North American Aerospace Defense Command (NORAD), the agency in charge of defending the country from missile attack, said, "We simply don't have a definitive answer at this time."
A spokesman for the Pentagon said that no missile could be launched without formal notification in advance to warn air and sea traffic, and no such notification had been received by any government agency.
The FAA also released a statement saying it had not authorized any launches.
A similar second vapor trail was reportedly seen by some witnesses Tuesday night off the coast as well.
The website contrailscience.com explains that the vapor trails left behind by jetliners can sometimes resemble a missile trail from some angles. In fact, at sundown Tuesday a similar trail streaked over Long Beach, but upon closer inspection, it's clear to see that it was coming from a jet.
As for Monday's mystery, one Pentagon official told ABC News they were going down the rabbit hole to look at every possibility from amateur rockets, although that would have been a big one to optical illusion.