Al Jazeera's Andrew Simmons, reporting from Gevgelija on the Macedonian side of the border, said the refugees were boarding trains to take them from Macedonia to Serbia.
The refugees hope that by taking trains through Serbia, they will make it to Hungary and other EU member states.
We are humans. We are not animals. We ran away from death and came here to die from the border police?
Syrian refugee on the border
Al Jazeera's Jonah Hull, reporting from Idomeni on the Greek side of the border, said the railway between the two nations was working again on Sunday.
"It is calm here. There is a free flow of movement as the Macedonian police allow small groups through," he said.
"There are lines and lines of refugees making their way to this point and there is no sign in the bigger picture that this flow is going to stop or slow down anytime soon."
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Police and security remained at the border on Sunday, checking the refugees belongings and bags as they allowed them to pass through.
"Heavy diggers at work are essentially clearing the ground alongside these railway tracks where over 2-3 acres are covered with human waste, abandoned tents, abandoned bags, clothing, children's toys, and empty bottles of water," Hull said.
Migrants sit on the train tracks and wait to cross the border near a train station in Idomeni, northern Greece [AP]
Our correspondent said that while hundreds on Saturday night had managed to cross the border by sprinting through open fields, many others had been sent back to Greece, where they alleged harsh treatment from Macedonian police and showed Al Jazeera their injuries.
One Syrian refugee told Al Jazeera what is happening to them is not what they expected when they fled Syria.
"We just want to pass or at least let those who are sick or with children pass. We are humans. We are not animals. We ran away from death and came here to die from the border police? Or from the cold?" the refugee said.
"Is it our fault there is fighting in our country? This is not fair.
"We are nothing to them, our passports are nothing to them. Imagine if this were you in our place, we have children. Don't you have children? Wouldn't you want the same?"
Children migrants look from a window on board a train departing towards Serbia, at the railway station in the southern Macedonia's town of Gevgelija [AP]
Ahmed Satuf, another refugee from Idlib in Syria, told Al Jazeera he didn't want anything from Macedonia, except for being allowed to cross its borders.
"I'm not a terrorist. We are humans. Where's the humanity? Where's the world? Everyone here, they are families," he said.
"We don't need anything. We don't need money. Let us cross. I want to go to Germany."
Source: Al Jazeera           copy       http://www.aljazeera.com/