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Izmailov, however, insisted that Politkovskaya would continue to inspire journalists at Novaya Gazeta. He said he and a team of younger journalists would pick up where she had left off and complete an investigation into the suspected misappropriation of budget funds from Chechnya that Politkovskaya had been working on before her death. "The work is continuing, but we are not ready to publish yet," he said.
Coincidentally, American journalist Paul Klebnikov, who was gunned down in Moscow in 2004, also was believed to have been looking into budget misappropriations in Chechnya.
http://www.moscowtimes.ru/stories/2006/10/10/003.html
I think it's rather paranoid for the IHT to imply that the government was somehow connected to the killing. If this was about misappropriation of funds, then that sounds like organized crime. There's plenty of that in Chechnya.