But the institute said a delay in reporting data from the large state of Saxony could be part of the reason for the sharp rise.
No Saxon data was transmitted on Monday, so Wednesday’s report includes missing data for both Monday and Tuesday.
The record daily increase in cases, set for December 11, is 29,875.
German leaders have sounded the alarm in recent days as the country faces a terrifying wave of coronavirus infections, hospitalizations and deaths.
The IRK chief said on Tuesday that the situation was “as serious as it has ever been during this pandemic”.
“At the moment, there are too many infected people,” said Lothar Wieler, who added that Germany must be prepared for “the situation to get worse during Christmas.”
German Health Minister Jens Spahn has joined several European countries in asking the European Medicines Agency (EMA) to approve the vaccine soon.
He said Germany would be ready to start vaccinating residents “two or four days” after approval.
“The goal is to get approval before Christmas,” Spahn told reporters at a news conference, adding, “We want to start vaccinating in Germany before the end of the year.”
President Frank-Walter Steinmeier addressed the nation on Monday in a rare speech, calling the situation “deadly serious.”
“As of Wednesday, our public and private lives will be more restricted than we have ever seen in the history of the Federal Republic of Germany,” he said, adding that “drastic measures” could not be avoided.
Merkel warned a week ago in the German parliament that the nationwide restrictions introduced on November 2 had been ineffective and action needed to be taken to prevent exponential growth in the figures.
“If we now have too many contacts before Christmas, and this will end up becoming the last Christmas with grandparents, we will have failed. We should not do that,” he said, in an unusually passionate speech.
The head of RKI’s surveillance unit, Ute Rexroth, reported an increasing number of infections and is likely to have died, saying Germany saw twice as many infections in care homes as during the first coronavirus rise in the spring of this year.
The shocking new figures are a cause for great concern and could cause the world’s fourth-largest economy to have another recession. It represents a strong warning to other countries struggling with a winter wave of the Covid-19.
An earlier version of this story dismissed the gap in Saxony figures released on Wednesday. They include Monday and Tuesday.
CNN’s Emma Reynolds and Nadine Schmidt contributed to this report.