With moments to go before the launch of an unmanned Soyuz rocket, officials had to postpone it early on Wednesday morning because a fault was uncovered with the rocket.
They rescheduled for 24 hours later, but there was uncertainty about whether the second attempt would go ahead.
The episode was the latest problem to beset Russia's space program, which Putin aims to revive as part of his push to restore Russia's military and technological might after years of post-Soviet neglect.
"The fact is there is a large number of hitches. That is bad. There should be an appropriate reaction," a stern-looking Putin was shown saying on state television at the Vostochny cosmodrome, hours after the launch was scrapped.
A handout picture shows a Russian Soyuz-2.1a rocket (AAP) Source: AAP
Delays and corruption have blighted work on the new cosmodrome, while this month a European Space Agency launch in French Guiana, using a similar Russian Soyuz rocket, was delayed by technical problems.
Problems with Russian space rockets are worrisome not just for the Kremlin but also for the United States space program. Since it retired its space shuttle, NASA depends on Russia to fly its astronauts to the International Space Station.
Russian news agencies later quoted state space commission sources as saying that a new attempt to launch the rocket from Vostochny would be made exactly 24 hours after the original one, at 0501 (0201 GMT) on Thursday.
Space tourist
Russia pioneered manned space flight when it fired Yuri Gagarin into space in 1961.
But since the collapse of the Soviet Union its space program has had to retrench for a lack of cash. For years it filled gaps in its budget by taking paying tourists into space.
The Vostochny spaceport, in the remote Amur region near the border with China, was the flagship project in Putin's planned $52 billion investment in space exploration up to 2020.
The first civilian rocket launch site on Russian territory, it is intended to phase out Russia's reliance on the Baikonur cosmodrome that Russia leases from ex-Soviet Kazakhstan.
Several people involved in building the Vostochny spaceport are under criminal investigation for embezzlement, workers went on strike over pay arrears, costs overran, and the project missed its scheduled completion date last year.
Speaking at the meeting with officials at Vostochny on Wednesday, Putin said he was satisfied to note that the cosmodrome was now in working order.
He said the technical glitch was to do with the rocket system, not the launch-pad, and that Russia still led the world in many aspects of space technology.
But he added that if suspects in the criminal investigation were found guilty, "then they will have to swap their warm bed at home for a prison bunk."
