Nurlan Shakiev said that Berezovsky's purported comments are also targeting "the dynamically developing Kyrgyz-Russian ties."
The "Delo No." weekly on November 29 published what it described as answers to written questions it had put to Berezovsky regarding his alleged relations with the top Kyrgyz leadership.
The newspaper quotes the exiled, London-based Russian businessman as admitting to recently visiting Bishkek for business talks and meeting with Bakiev's son, Maksim.
Bakiev has denied earlier reports that said Berezovsky secretly flew to Kyrgyzstan on July 29.
Russian authorities last month reportedly asked Kyrgyz officials to explain how Berezovsky, who is wanted on an international warrant, could have entered the country without being arrested.
Russia accuses Berezovsky of fraud and other criminal offenses that he denies.