Spokesperson Andriy Yusov made the comments about the death of Maxim Kuzminov to Ukraine's public broadcaster but did not provide further details.
Spain's EFE news agency reported that a body found on February 13 in Villajoyosa, near Alicante in southern Spain, was that of Kuzminov, citing sources close to the investigation.
EFE reported that Kuzminov —who landed in Ukraine in a fully equipped Mi-8 helicopter last August — had been living in Spain with a Ukrainian passport but under a different identity.
At the time of his defection, Kuzminov said he had been offered security guarantees, new documents and a reward.
Two Russian crew — who were also on the flight but unaware of the plan to defect — were killed after landing, according to Ukraine's military intelligence.
"In Russia it is customary to speak either good of the dead or nothing at all," Sergei Naryshkin, the director of Russia's Foreign Intelligence Service (SVR), was quoted in Russian media as saying when asked about Kuzminov.