"A limited number of illegal migrants in vulnerable categories are allowed to enter Macedonia and they may be provided with aid in accordance with the state's capacities," the interior ministry said in a statement.
It did not elaborate on what it considered vulnerable categories, but shortly after the announcement, Macedonian police allowed in a few hundred refugees, mostly families with children and pregnant women.
Police issued temporary transit documents to 181 migrants, mostly from Syria, Bangladesh and Pakistan, wanting to cross the small Balkan country on their way to northern Europe in the last 24 hours, the ministry statement said.
"Police allowed us to enter into the country," a 17-year-old Syrian called Salim told AFP, saying he was travelling alone as his family had stayed in a refugee camp in Turkey.
The move however caused tensions among many of those being prevented from crossing, an AFP reporter said.
Many said they had spent two days in no-man's land after Skopje decided on Thursday to seal the border and declared a state of emergency.
Walking along the railroad they headed to the train station in the Macedonian town of Gevgelija, where they hope to catch a train and continue their trip towards Serbia and EU borders on the north.
More than 3,000 mostly Syrian refugees are -stuck in no-man's land near the Greek village of Edomeni in a standoff with police and troops sent by Skopje to help stem the flow of migrants attempting to cross into Macedonia.
Before Macedonia declared a state of emergency on its southern border on Thursday it was issuing an average of 1,300 such documents a day, it added.
More than 41,000 migrants have been processed since mid-June.
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