Two of the representatives of Bosnia's presidency not present at the meeting say Lavrov should have started his visit in the capital Sarajevo rather than the Serb part of the country.
Bosnia's Muslim and Croat representatives in the country's three-member presidency have boycotted a meeting with Russian foreign minister Sergei Lavrov, accusing the diplomat of "disrespect" towards their state.
Lavrov had been due to hold talks with members of the Bosnian presidency on Tuesday on the second day of his visit, but only the Serb representative, Milorad Dodik, was present.
Bosniak Muslim representative Šefik Džaferović and Croat Željko Komšić both boycotted the meeting in a major snub to Moscow.
The two men argued that Lavrov should have started his official visit on Monday in Bosnia's capital, Sarajevo, instead of in the Serb semi-autonomous half of the country. No Bosnian flag was present and the Russian foreign minister also hailed Dodik's comments that Bosnia will remain militarily neutral and will never join NATO.
"Lavrov knows that only the state can make such decisions," Komšić said at a joint press conference with Džaferović.
"With respect to the Russian Federation as a big and powerful country, we will not agree to become a Russian pawn in the Balkans in their games and conflicts with the EU countries or NATO member countries".
"We expect them to understand and support this," Komšić added.
Lavrov did not comment on the boycott on Tuesday, and the Russian foreign ministry posted a photo without mentioning that two out of three presidency members were not present.
The Russian foreign minister's visit coincides with the 25th anniversary of the US-mediated Dayton peace agreement that ended a four-year war in Bosnia in the 1990s.
Although the deal ended fighting, it divided Bosnia in half between the Bosnian Serb Republika Srpska and the Muslim-Croat Federation.
Lavrov said on Monday that the agreement must not be changed, in reference to comments by Western diplomats and Bosnian politicians that the Dayton peace accord needed upgrading for Bosnia to make progress on reforms.
"I would like to say that any attempt to demolish (the Dayton agreement) can cause the most serious risks and consequences," Lavrov said.
Bosnia’s foreign minister Bisera Turković also signed an agreement with Lavrov on future cooperation on Tuesday.