The mishap is the latest blow to the Russian government's plans to overhaul its famed space programme after a series of setbacks.
The next-generation Angara rocket was scheduled to blast off from Plesetsk in northern Russia when officials reported a sudden automatic launch abort, footage of which was broadcast on national television.
The Kremlin strongman, who was overseeing the rocket's planned launch via live linkup, gave space officials and the defence ministry an hour to look into the glitch before reporting to him.
The launch has been postponed until tomorrow.
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Designed to succeed Proton and other Soviet-era launchers, the Angara is billed as the first rocket to have been completely built after the collapse of the Soviet Union.
Officials say the next-generation spacecraft is more environmentally friendly than its predecessors because it is fuelled by oxygen and kerosene rather than hugely toxic heptyl.
The Khrunichev Center, the state-run spacecraft maker which developed the rocket, declined to say what went wrong.
"We can't say anything right now. The defence ministry will be looking into this," a spokeswoman told AFP.
But more recently, the programme has been hit by a number of setbacks, notably losing expensive satellites and an unmanned supply ship to the International Space Station.
Today's mishap comes after a Proton launcher carrying an advanced communication satellite fell back to Earth minutes after lift-off in May.
Last July, an unmanned Proton carrier rocket exploded on takeoff at the Baikonur cosmodrome in Kazakhstan, releasing hundreds of tons of toxic fuel in spectacular images caught on live television.