"More than 3000 refugees are gathered at the Greece/FYROM borders, tensions are high, #MSF teams treating injured people with shrapnel wounds," the organization said on Twitter.
Earlier in the day, Greek media reported that Macedonian police had fired stun grenades and tear gas to disperse the crowds that formed due to the border between the two countries being shut on Thursday.
The Macedonian government declared a state of emergency along the country's southern and northern borders on Thursday and said it would deploy the army to deal with the huge numbers of migrants on the border.
Europe is currently facing a major migrant crisis, as thousands of undocumented asylum seekers from conflict-torn countries in North Africa, the Middle East, Central and South Asia are arriving in Europe, hoping to escape poverty and violence in their home countries.