"This, of course, is the height of fakery," Foreign Ministry spokeswoman Maria Zakharova said.
The comments came after The Associated Press said that three Indonesian government and medical officials told them that the Russian diplomat was being treated on the resort island.
The officials said he was taken to Sanglah Hospital in the provincial capital, Denpasar. The hospital did not immediately comment.
Bali Governor I Wayan Koster was quoted as saying on Monday that Mr Lavrov was in good health after he was taken to a hospital for a medical check-up and that he had left "immediately".
Amid the reports on Monday, Mr Lavrov told the Russian TASS news agency that he was in a hotel preparing for the G20 summit.
Mr Lavrov is representing Russian President Vladimir Putin at the summit of world leaders and arrived in Bali on Sunday after participating in meetings hosted by the Association of South-East Asian Nations in Cambodia over the weekend.
Russia's February 24 invasion of Ukraine sparked calls by some western leaders for a boycott of the G20 summit and for the withdrawal of Mr Putin's invitation.
But Indonesia, closely associated from the 1950s with the formation of the Non-Aligned Movement, has instead focused on its "bebas dan aktif", or "free and active" foreign policy.
The position of non-alignment was born out of the Cold War to try to keep the peace amid the global fractures, analysts said.
Indonesia has held its ground on Russia, refusing to withdraw Mr Putin's invitation and also rejecting what Indonesian sources say has been pressure from G7 countries to condemn Russia at the summit this week.