"This is all very bad. This is an absolutely unacceptable political murder, and it will lead to further escalation of tensions," Deputy Foreign Minister Mikhail Bogdanov told Russia's state-run news agency, RIA Novosti.
What happened will have a significant negative impact on the Doha negotiations, Bogdanov warned.
The Palestinian resistance group Hamas announced early Wednesday that Haniyeh was killed in an Israeli airstrike targeting his residence in Tehran.
Israel has made no immediate announcement about the assassination.
Iranian state television also reported Haniyeh’s death, noting that an investigation into the assassination is ongoing and that the results will be announced soon.