"Even now, speaking to you, I am afraid to say anything positive about the American president," Russia's envoy to the U.S. told reporters in Moscow.
Flynn resigned as Trump's national security adviser in February.
The newly appointed ambassador spoke before the current U.S. government announced further sanctions on Russian diplomats.
According to sources, Sessions will also dispute the account Comey gave under oath of a conversation between the two men.
The House Intelligence Committee chairman has made it clear his allegiances are with Trump, not Congress.
Pro-government newspapers say the assassin was sent to disrupt Syria negotiation.
The department said the situation with U.S.-based cleric Fethullah Gulen had no bearing on the assassination.
Fethullah Gulen called Ambassador Karlov's killing a "heinous act of terror".
Around 18 Russian experts will assist the investigation into Ambassador Karlov's shooting.