However, FIFA denied a comment attributed to President Sepp Blatter, who was quoted a sport agency as saying "you can be sure about this" in reply to a question about whether the two countries would be kept apart.
"The President did not say that they would be kept apart or that such a decision has been made. It seems (there was) a translation mistake," said FIFA in a statement.
"What the FIFA president actually said was that, in any qualifying campaign, the aim is always to avoid problems as was done in the past between teams where high tensions can be anticipated,” the statement added.
"On Ukraine/Russia situation, he said that we have to see how this evolves but, if the geopolitical situation were to remain as it is now, when it comes to the final competition then FIFA could decide that the respective teams would not be in the same group,” it further said.
Blatter, who was on a visit to Moscow for the unveiling of Russia's official World Cup emblem, said politics should not mix with sport following calls to move the 2018 tournament to a different country due to Russia's conflict with Ukraine.
"A boycott never achieves anything and does not have a positive effect. FIFA is fully supporting the World Cup in Russia," said the 78-year-old in an interview.
"When we received letters from North America, we answered that this is football. We believe in the country (Russia) and their government,” he added.
"The mass media should help us with this. We have experienced such things in the past at the Sochi Olympics. However, during and after the (Winter) Games there was not one bad word written about the event,” he further said.
"You know, Russia is in the focus of the world press. Football cannot only unite Russia, but can also show the whole world that it is stronger than any protest movement," Blatter said.
Blatter said he was pleased with Russia's preparations for the tournament.
"In comparison with Brazil's preparations for the 2014 World Cup, Russia is well ahead of them with four years to go,” he said.
He said the third place playoff will be kept despite calls from teams to abolish it.
"We will not be getting rid of it. It's very important. If there was no third place playoff then the head of (European body) UEFA, Michel Platini, would never have taken home a bronze medal. These games are always well fought," the Swiss said. 
Putin says needs effective, yet subtle World Cup security

Meanwhile, Russian President Vladimir Putin said on Tuesday security at the 2018 World Cup would be "effective but not intrusive", underlining to his security chiefs the need for subtle measures that will not scare off fans.
At a meeting of Russian and FIFA officials, Putin won support from Blatter for Russia's staging of the football championship despite calls by some Western officials to move it elsewhere because of Moscow's role in Ukraine.
Putin urged the security services to work together to make sure the tournament, to be staged in 12 stadiums in 11 Russian cities at a cost of 664 billion roubles (USD 15.6 billion), passes off without problems.
"Here there should be complete cooperation, coordination of work of all services and departments. It should be marked for personal responsibility," Putin told a meeting of Russian, regional and FIFA officials.
"Security measures should be effective, but not intrusive, not excessive," he said.

"Do not create problems, or discomfort for athletes and fans,” he added.
Although winning the right to host the World Cup stirred national pride, Moscow has faced calls for the finals to be played elsewhere because of its role in the Ukraine crisis and some Western officials have suggested a boycott.

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