Compared with the more than 7,000 asylum seekers who were arriving each day in recent weeks, the police counted only 2,650 on Saturday and 3,136 on Sunday.
Of the 5,786 who arrived over the weekend, 4,208 entered the country in Bavaria, reports Reuters.
A spokesperson for the Interior Ministry said that strong winds in the Aegean Sea, where asylum seekers travelling from the Middle East make the crossing from Turkey into Europe, could be one cause of the drop in numbers.
Another reason for the fall in arrivals could be the border controls set up at by various countries along the so-called ‘Balkan route' the route through Europe taken by most refugees which passes through the Balkan region.
Slovenia, for example, has only been letting Syrian refugees pass through the country for the past two weeks.
At the Austria-Slovenia border, the flood of asylum seekers has also reduced to a trickle. On Monday at midday there were no refugees on the Slovenian side and only ten on the Austrian side.
So far 216,000 asylum seekers have arrived in Germany in November, according to police numbers, making it by some distance a record month for the number of new arrivals.
In November the government's forecast for 800,000 arrivals in 2015 has also clearly been overstepped.