During a livestream of Sunday's launch, SpaceX said it got successful confirmation that the fairing - the clamshell-like covering for payloads at the tip of the rocket - did deploy.
The nature of the mission remains shrouded in mystery.
Northrop Grumman, the aerospace and defense company that built the Zuma spacecraft, would only say: "This is a classified program. We can not comment on a classified mission", he said.
The Wall Street Journal was the first to report late Monday that the billion-dollar payload did not make it into orbit and was "presumed to be a total loss", citing unnamed government and industry officials.
The Journal, which received the same statement, said the language pointed to normal rocket operations, suggesting the cause of any issue came from elsewhere.
A USA official and two congressional aides, all familiar with the launch, said on condition of anonymity that the second-stage of SpaceX's Falcon 9 booster rocket failed.
"If we or others find otherwise based on further review, we will report it immediately", she said. Information published that is contrary to this statement is categorically false. "We do not comment on missions of this nature, but as of right now reviews of the data indicate Falcon 9 performed nominally", a representative for the company said.
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"Since the data reviewed so far indicates that no design, operational or other changes are needed, we do not anticipate any impact on the upcoming launch schedule", Shotwell added.
Falcon Heavy-a modified variant of the Falcon 9 and equal to approximately eighteen 747 aircraft at full power-is due to be rolled out at the Kennedy Space Center in Cape Canaveral, Florida, for static fire tests later this week.
Falcon Heavy is SpaceX's massive new rocket that will boast three times the thrust of the Falcon 9. Earlier in the day, SpaceX founder Elon Musk shared photos of the nighttime launch on Twitter.
SpaceX typically supplies such an adapter but reportedly did not for this mission. A standard Falcon 9 rocket launch costs about $62 million, and this was SpaceX's third national-security launch.
SpaceX competes for military launches with United Launch Alliance, a joint venture of Boeing and Lockheed Martin Corp., which was the sole provider for the Pentagon until Musk launched a campaign in Congress and the courts challenging what he called an unfair monopoly. Additionally, a SpaceX rocket carrying supply missions to the International Space Station for NASA exploded in 2015. The company has recently ramped up its launch pace, even launching two missions from opposite coasts within about 48 hours.
The loss of a government payload comes at a bad time for SpaceX, which was founded by Elon Musk, who is CEO of both the privately-held rocket company and electric auto maker Tesla.