The 4,000km pipeline has the capacity to deliver over two million barrels a day, of which about 1.4 million to 1.6 million go directly to consumers in the EU.
The Kremlin has said that Russia received notification that Belarus had imposed a transit duty on its oil exports, but said it did not expect a growing trade row to disrupt crude shipments to Europe.
Belneftekhim, a large state Belarusian industrial and energy holding company, ordered the suspension of transit of oil to Germany, Poland and Ukraine.
The economics ministry in Warsaw has said the dispute between Moscow and Minsk is the cause of disruptions in oil deliveries from the pipeline that crosses Belarus.
Piotr Naimski, Poland's deputy economy minister, said, "This shows us once again that arguments among various countries of the former Soviet Union, between suppliers and transit countries, mean that these deliveries are unreliable from our perspective."
The German government confirmed that the pipeline, which supplied two refineries in Germany, had been shut down.
"I can confirm the Druzhba pipeline has been closed ... we are trying to ascertain the reasons," Hendrik Luchtmeier, a German economic ministry spokesman, said.
The impact of a short-term stoppage in Poland and Germany is likely to be minimal, as refineries maintain strategic oil stocks.
Andris Piebalgs, the EU's energy commissioner, said that the cut in Russian oil shipments to the EU posed "no immediate risk" to energy supplies in the EU.
He said that he was seeking an "urgent and detailed explanation" of the cuts from authorities in Belarus and Russia.
The EU energy chief said he was considering calling a special meeting of energy experts from the 27 EU nations to discuss the situation in case they had to draw on oil stocks.
Several countries in the EU, which depends on Russia for 25 per cent of its gas supply, suffered a brief disruption early last year after Moscow suspended gas deliveries to Ukraine because of a pricing dispute.
The suspension of oil deliveries comes only days after Belarus and Russia reached an agreement on gas prices that avoided a natural gas cut-off for Belarusian consumers.
Belarus grudgingly accepted a doubling of the price it pays for imports of Russian natural gas, on which it depends for industry and home heating.
The two countries are now in dispute over oil duties, with Russia determined to stop Belarus from re-exporting petroleum products made from processing Russian oil bought cheaply.
A spokesman for the EU energy commission said that Poland had about 70 days of reserves and Germany 130 days.