On Sunday, 8,540 people entered the country via the Nickelsdorf crossing point with Hungary, followed by another 3,680 between midnight and 7:00 am on Monday, they said.
The total is higher than in recent days, with daily totals over the previous week averaging around 5,500, the vast majority of whom seek to travel onwards to Germany and elsewhere.
Police spokesman Gerald Koller told AFP that the increase follows a recent rise in numbers entering Macedonia from Greece on their way northwards through Serbia, Croatia and Hungary.
"This is not a record, though. There were days last month when we had daily totals of 12,000 or 14,000," Koller said.
Hungarian police said 7,879 migrants entered the country on Sunday and 7,907 on Saturday, also higher than the average of previous days.
Europe's biggest influx of migrants has seen several hundred thousand people enter the continent this year, many fleeing conflict in Syria, Iraq and Afghanistan.
The crisis has exposed deep divisions within the 28-nation European Union over how to distribute the new arrivals and stemming the flow, as well as a rise in popularity for nationalist parties.