“This is very, very frustrating," Soeder said in a tweet late Wednesday. “It must be immediately fixed.”
Already, state Health Minister Melanie Huml said that officials had worked through the night on the results and promised that all of those who tested positive would be informed Thursday.
Bavaria has been offering free voluntary tests at airports, as well as specific train stations and highway rest areas, and has carried out some 85,000 since the end of July, Huml said.
The interest was higher than expected, and the delays were almost exclusively at the rest areas and train stations where some 60,000 people were tested since July 30.
Those operations were initially run by voluntary organizations, which had been manually entering details into computer spreadsheets.
The Bavarian Red Cross, one of the agencies involved, said they had been given one day to set up five test stations, and that the Health Ministry had provided no software, so they had to rely on what they had.
The head of the state Red Cross, Wolfgang Obermair, said it was “regrettable” that his and other aid organizations were being painted in a negative light.
The stations are all now being taken over by private companies, which Obermair said had been able to work on streamlining the process over the past two weeks.
Soeder, who has national political aspirations, has been widely criticized for the failure to ensure people were promptly informed of the test results.
“Anyone who constantly portrays himself as a crisis manager as governor and regularly pats himself on the back is also responsible for ensuring that everything works,” Annalena Baerbock, co-leader of the Greens, told the dpa news agency.
Federal Health Minister Jens Spahn defended Soeder, telling ZDF that the delay in communicating the results of 44,000 tests was “annoying, without a doubt” but that Bavaria was heading in the right direction.
“Basically I'm very grateful that we are testing so extensively and that Bavaria also makes it possible to take tests at rest stops when entering the country by car,” he said. “But then, of course, the results have to be transmitted.”
It was not yet clear which countries the people who tested positive were from, nor where they were staying.
Germany has widely been seen as a success story in managing to quickly slow the spread of the pandemic, from a peak of more than 6,000 new cases daily in late March and early April to the low hundreds.
The numbers have been rising recently, however, with the country's disease control center, the Robert Koch Institute, reporting 1,445 new cases on Thursday.
The figure has topped 1,000 several times recently, and Spahn on Wednesday said smaller and mid-sized outbreaks have occurred in almost all regions, largely driven by travelers returning from abroad and people partying or having family gatherings.
As of Saturday, any travelers arriving from high-risk areas have been required nationwide to take coronavirus tests.