Ukrainian authorities denied entry to Sergei Markov at the airport Thursday, without explaining the reasons for the move.
"The Ukrainian authorities have once again decided to resort to a practice that is probably becoming the favorite one in the arsenal of anti-Russian actions by modern-day official Kiev - to ban entry to the country to Russian politicians, including parliament deputies," the ministry said.
"Moscow has become tired of repeating that the method of drawing up 'blacklists' actively used by Kiev is a totally vicious practice only complicating the development of bilateral ties," the ministry said.
Media have suggested that Markov was banned from entering Ukraine because President Viktor Yushchenko did not want to hear questions Markov could pose him at a historical conference in Ukraine.
"The desire to ban the Russian researcher from [the conference] does not do honor to the Ukrainian authorities, who are clearly avoiding a competent and specific public discussion on the problems of our own common history," the Russian ministry said.
The ministry said several other Russian public figures were on Ukrainian entry blacklists. They include deputy Russian lower house speaker Alexander Babakov, deputy chairman of the CIS affairs committee Konstantin Zatulin and MP Viktor Vodolatsky.
In July, Zatulin was banned from entering Ukraine.
Although the Ukrainian authorities insisted that Zatulin leave the country, they declined to provide him with a ticket. The Russian MP refused, as a matter of principle, to pay for his return flight.
"If, God forbid, I was sentenced to be shot, I would not be obliged to pay for the bullet and the services of the firing squad," Zatulin said then.
Zatulin, along with outspoken fellow MP, Vladimir Zhirinovsky, had earlier been listed as a persona non grata by Ukrainian authorities after his involvement in 2006 protests in the Crimea against joint NATO-Ukraine Sea Breeze military exercises in the Black Sea.
Zatulin's persona non grata status was annulled however when Moscow and Kiev mutually scrapped lists of "undesirables" in 2007.
Ukraine's state security services barred Moscow Mayor Yury Luzhkov on May 12 from entering the former Soviet republic over his "provocative" comments regarding the ownership of Sevastopol. Moscow's mayor also made strong calls for a naval base in the Black Sea city to be handed back to Russia.