At Frankfurt Airport, the largest hub in the country, 40 flights were cancelled and countless delays expected, spokesperson Gunnar Schenuemann said.
In Berlin, all flights by low-cost airlines EasyJet and Germanwings leaving from the Schönefeld Airport were cancelled due to a shortage of de-icing materials. A truck with fresh supplies was reportedly caught in a traffic jam caused by the snow on Thursday.
GlobeGround, which de-ices planes at the German capital's two main airports Tegel and Schönefeld, said that manufacturers were experiencing "drastic" problems not only in delivering to airports but also in production.
"GlobeGround's de-icer stocks have fallen dramatically. There are currently nine orders for Tegel and Schoenefeld that have not been made, many of them were supposed to have come two days ago," it said.
Air Berlin, Germany's second-biggest airline after Lufthansa, said that there had been shortages in recent days, but that the situation had returned to normal on Friday.
"We think it is a structural problem. There are only a few firms in Europe (who make de-icer), leading to shortages across Europe, which could become a problem this winter," a spokeswoman told news agency AFP.
Schönefeld spokesperson Leif Erichsen said flight schedules for other airlines were expected to return to normal by midday.
EasyJet recommended that passengers check their website to find out whether their flight had been cancelled, and offered refunds or complimentary booking changes.
Meanwhile snow continued to blanket the country, with another 10 centimetres expected in the Alps within 12 hours, the German Weather Service (DWD) reported.
The mountains could also see storm winds of up to 80 kilometres per hour that will likely lead to drifting.
Drivers should remain cautious due to quickly forming black ice on roads, the DWD said.
In the state of Saxony-Anhalt police reported 426 traffic accidents on Thursday, with two deaths and 36 injuries.
Snow drifts in the region reached almost two metres along roadways, creating traffic jams lasting for hours as many drivers abandoned their vehicles.
Snow and ice also snarled traffic on the A3 and A48 motorways in the state of Rhineland-Palatinate near Montabaur, police said.
In North Rhine-Westphalia police reported 359 accidents in the last 24 hours, with four severe injuries and damages estimated at almost €750,000.
In Bavaria police said they reported to about 100 accidents near Regensburg between Thursday afternoon and Friday morning. One young woman was killed in a collision, and another six were injured in separate accidents.
But conditions had improved slightly around Heidelberg, in the southern state of Baden-Württemberg, where police were able to reopen the B37 motorway after a 24-hour closure due to flooding by the Neckar River.