"In no case should the lunar program be interrupted, that would be the worst decision," Yuri Borisov said in an interview on television.
The Luna-25 mission was meant to mark Moscow's return to independent Moon exploration in the face of financial troubles and corruption scandals and growing isolation from the West.
But on Sunday, Roscosmos announced the probe had crashed during pre-landing manoeuvres.
"Interrupting the lunar program for almost 50 years is the main reason for the failure" of Luna-25, Borisov said.
"The invaluable experience that our predecessors accumulated in the 1960s and 1970s was practically lost" during the interruption of the programme, he added.
Borisov explained the crash was due to an issue with the spacecraft's correction engine.
The engine supposed to put the spacecraft into pre-landing orbit "worked for 127 instead of the planned 84 seconds. This was the main cause of the probe's crash," Borisov explained.
A special commission has begun looking into the exact causes of the incident, Borisov also said.
Moscow last landed a probe -- Luna-24 -- on the Moon in 1976, before shifting away from lunar exploration in favour of missions to Venus and building the Mir space station.
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