The launch was aborted and the two-man crew, Russian cosmonaut Alexey Ovchinin and NASA astronaut, Nick Hague, were blasted free of the rocket inside their capsule and hurtled back to Earth, falling from nearly 40 miles.
NASA and Roscosmos said search-and-rescue teams were in contact with the crew and en route to the landing location. But it is also unlikely any Soyuz missions will fly for a while now until both NASA and Roscosmos, the Russian space agency, have got to the bottom of what went wrong today.
Hague, who only joined NASA's astronaut corps in 2013, was on his first space mission.
Russian Federation now operates the only spacecraft for ferrying crews to the station following the retirement of the USA space shuttle fleet, but it stands to lose that monopoly in the coming years with the arrival of commercial US crew capsules - SpaceX's Dragon and Boeing's Starliner.
A tweet from Roscosmos shows the two astronauts resting comfortably, and looking like they're in good spirits, despite what must have been a hard experience.
The failed launch earned scathing criticism from the usually pliant Russian media.
Rogozin was flying to the scene of the emergency landing, the space agency said. The station is now stocked with sufficient supplies for six months and can be re-supplied by unmanned cargo ships.
"A thorough investigation into the cause of the incident will be conducted", Bridenstine said, saying the safety of the crew was the utmost priority for NASA.
Wiseman said the astronauts were alerted about one second in advance by a warning light inside the capsule before it was separated from the malfunctioning Soyuz rocket.
NASA said: "There's been an issue with the booster from today's launch". Eric Berger ofArs Technica reports that Russian sources said the failure occurred about two minutes into flight, suggesting the rocket had a problem during second stage separation, but the exact nature of the complication is unknown.
In August, the space station crew found a hole had been drilled in the Soyuz capsule that caused a brief loss of air pressure before being patched.
Questions are now likely to be asked about Russia's space program. For now, the two astronauts are safe as are NASA astronaut Serena Auñón-Chancellor, German astronaut Alexander Gerst and cosmonaut Sergey Prokopyev.
David Saint-Jacques is scheduled to co-pilot the capsule December 20 and become the first Canadian at the orbiter since now-retired astronaut Chris Hadfield returned to Earth in 2013. Spacewalks take extensive, long-term planning, so the crew and their teams back on Earth will have to come up with an alternative plan.
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