A Russian spy at the center of a secret operation to smuggle high-tech weapon components into Russia has left Japan after his activities were disclosed by The New York Times, a senior Ukrainian intelligence official said on Thursday.

The operative, Maksim Vladimirovich Filchenkov, 49, had been working undercover in Japan as an employee of the Russian state airline Aeroflot. Mr. Filchenkov’s role had been the focus of a Times investigation into how Russia exploited Japan’s weak espionage laws.

Mr. Filchenkov’s departure was first reported by Yomiuri Shimbun, a major national newspaper in Japan. The newspaper said the Russian exited Japan after The Times published its investigation on July 12. The Ukrainian official who confirmed the spy’s departure did so on condition of anonymity because he was not authorized to discuss intelligence publicly.

The Russian spy’s presence in that country had frustrated Ukraine, which had repeatedly warned that, despite Japan’s export restrictions and economic sanctions, its high-tech components were still being shipped to Russia. Ninety percent of Russian missiles and drones contain Japanese components, according to Ukrainian government estimates.

Mr. Filchenkov was part of a clandestine unit known as the 20th Directorate of Russia’s military intelligence agency, the G.R.U. Posing as diplomats or businesspeople, its officers work to buy or steal battlefield technology and smuggle it into Russia.

That made Mr. Filchenkov, a veteran officer who had previously served in Japan, a key cog in supplying Russia’s war machine as he formed business relationships with logistics companies that ship goods from Japan to Russia, often through intermediary countries.

Mr. Filchenkov has not responded to messages seeking comment. He declined to meet with reporters who visited the Aeroflot office earlier this year.

The Japanese government has not directly addressed questions about him or the 20th Directorate but said that the Times report showed the need to better combat foreign espionage. Minoru Kihara, a top Japanese cabinet official, said the country “must address this issue with even greater rigor.”

Japan is working to build an intelligence agency, which it has not had since World War II.

Former intelligence officials familiar with Russian intelligence operations say that spies whose identities have been revealed often return to Moscow and work desk jobs or train future generations of spies — meaning Mr. Filchenkov’s undercover days are likely over. But officials say that the 20th Directorate remains a key part of the Kremlin’s effort to obtain weapons components.