President Vladimir Putin's spokesman Dmitry Peskov told journalists: "In this case you should not waste your breath talking about some kind of politicisation, censorship and so on. Such discussions are absolutely inappropriate and have nothing to do with purely financial questions."
The Kremlin spokesman was giving his first in-depth comment on the case.
Serebrennikov, creative director of the Gogol Centre theatre in Moscow who has also staged productions at the Bolshoi theatre, is under house arrest after being charged last week with defrauding the state of 68 million rubles (USD 1.15 million) in funding for a theatrical project, for which he could face a decade in jail. He denies any guilt.
The case has caused an uproar in the arts world in Russia and beyond, with many linking it to Serebrennikov's criticism of increasing state censorship of the arts.
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Peskov, however, dismissed the support Serebrennikov has received from colleagues in the theatre.
"The support from colleagues... Is very understandable, but probably you should not link this support directly to those questions that investigators have for Serebrennikov," he said.
One of Russia's best known actresses and philanthropists, Chulpan Khamatova, who once made a video supporting Putin's election campaign, spoke out against his arrest at an awards ceremony today.
A court has detained Serebrennikov under house arrest in Moscow until October 19, despite numerous offers of bail from his supporters including the sister of billionaire Mikhail Prokhorov.