"This decision must be carried out, taking into account the appeals and the worries."
The highway was planned to go from Moscow to Saint Petersburg along the increasingly jammed route to the Sheremetyevo international airport.
Plans to build the motorway have long angered local residents.
Environmentalists insist there are several options for the route to bypass the forest.
Vladimir Putin, the Russian prime minister and the leader of United Russia, made an unprecedented appeal to Medvedev to halt the project.
"United Russia has turned to the president of Russia ... with the request to halt the construction of the highway through the Khimki forest," Boris Gryzlov, the party's chairman, said in a statement.
"We have different opinions within United Russia about this question. But the situation does not look simple."
This week, at least 2,000 people, including Russian rock stars and leading rights activists, attended a concert in central Moscow criticising the government's plans.
This protest was much larger than previous opposition protests where unsanctioned rallies have been characterised by thin turnouts and police crackdowns.
"This is our victory," Andrei Morgulyov, head of the Union of Environmental Non-governmental Organisations, told the Associated Press news agency.
"This decision would have never happened if we were not fighting for our cause."
Morgulyov, who was among a group of activists who set up tents in the forest this summer to protect the trees, said he was confident the plans to build the highway would soon be scrapped.
Speaking to the AFP news agency, Yevgenia Chirikova, the activist who has led the protest movement against the motorway, said: "We are very happy. But it is hard to explain because until now the authorities were not reacting to the civic protests."
The editor of a Khimki newspaper who reported extensively on the issue was severely beaten in 2008 and left crippled. His attackers were never found.