"The first manned flight from the Vostochny Cosmodrome is scheduled for 2025 with an Angara-AV5 rocket, according to the federal space programme," agency spokesman Mikhail Fadeyev told AFP.
A 2007 presidential decree had said that the first manned launch from the cosmodrome, which is being built in the far eastern Amur region, would take place in 2018.
But the deadline outlined in the decree would have forced the space agency to adapt the new cosmodrome to aging Soyuz rockets, which are expected to be replaced by new Russian-made Angara rockets by 2024.
The decision to postpone the first manned flight from the new cosmodrome, according to Fadeyev, reflects the "founding principle of Vostochny as an innovative cosmodrome" and has been approved by the "highest echelon" of government.
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Developing the Angara has cost Russia at least $2 billion since the early 1990s, sparking criticism over its high cost.
Space agency head Igor Komarov said in April that the space programme's budget for 2016-2025 would receive a 800-billion-ruble (USD 11.3 billion) haircut.
Hailed by President Vladimir Putin as the country's biggest construction project, the Vostochny Cosmodrome has an estimated budget of 300 billion rubles (USD 4.2 billion at the current exchange rate).
Construction at the cosmodrome has been plagued by labour disputes, corruption scandals and delays in the last months. Unpaid construction workers protested their employment conditions and appealed to Putin during his annual call-in show in April.
The first unmanned launch from the cosmodrome is schedule to take place in December.