Gilbert Felli , the IOC's executive director, said:"Vladimir Putin has proposed changes that will help minimise the environmental impact during the construction and operation of the Olympic transport facilities.
"And we have gratefully accepted the proposal."
Russia's Prime Minister had said in July that construction of some venues for the 2014 Winter Olympic Games in Sochi should be moved from a national park to alternate sites to avoid damaging the environment.
In its final report on the Sochi 2014 Winter Olympics, the United Nations Environment Programme confirmed in June that the proposed construction of bobsleigh tracks and an Olympic village on the Grushevy Ridge could cause environmental damage to the mountainous conservation area.
Environmental groups said earlier this year that the planned bobsleigh route was potentially one of the most harmful Olympic projects.
Other top concerns were the alpine Olympic village and a rail link in the region, classified by UNESCO as the only mountainous area in Europe that remains virtually untouched by humans.
Putin, who as President was a major factor in Sochi's victorious bid to host the Olympics, said the region's infrastructure should be developed in accordance with environmental considerations, but without delaying the construction of the Olympic facilities.
Russian Regional Development Minister Dmitry Kozak said that some 500 million rubles (£10.8 million) had been allocated specifically to meet environmental needs during the Olympic construction.
Sochi won the right to host the Olympics at an IOC session in Guatemala in July 2007 after a close race with South Korea's Pyeongchang and Austria's Salzburg.
Russia will be hosting the Winter Olympics for the first time in 2014. Moscow hosted the Summer Olympics in 1980, but the event was marred by a United States led boycott involving more than 60 countries.