Only those with a valid reason for travel, like cross-border commuters and delivery drivers, are allowed through, officials said. The measures started at 7am, AFP reporters said, and reportedly started at 8am at the border with Denmark.
At the border between Germany's Kiefersfelden and Austria's Kufstein, police let trucks through but stopped all passenger cars to question drivers, AFP photographers saw.
By 7.30am some 10 cars had been turned back.
German citizens and people with a residency permit will still be allowed to return to the country, Interior Minister Horst Seehofer said on Sunday when he announced the temporary border checks.
“The spread of the coronavirus is progressing quickly and aggressively…one of the most important measures will be to cut off the chain of infection,” Seehofer told reporters as he announced the new border controls.
People “without a significant reason to travel” and those suspected of having been infected with the virus will not be allowed to cross the affected borders, he said.
Seehofer stressed the new controls would be temporary, and would be reassessed “from time to time”.
But the high point of the coronavirus crisis had not yet been reached, he warned, urging citizens to avoid social contact.
The decision had been taken after the Robert Koch Institute, which is responsible for public health in Germany, had declared that the French border region of Alsace-Lorraine as a risk area.
“This sparked a lot of questions and unrest in the neighbouring states,” he said.
A source close to the matter had told AFP earlier on Sunday about the planned border closures, confirming a report in the German media.
The popular tabloid Bild had reported that the closures would take effect on Monday.
Closing borders was not only to contain the COVID-19 epidemic but also to prevent panic bulk purchases by foreigners, which was apparently causing supply problems in areas around the borders, according to Bild.
Latest drastic measure
It is the latest drastic step taken by German authorities to halt the pandemic.
From Monday, schools and daycare centres in most German states will remain closed, with some exceptions made for parents in critical jobs who have not yet found alternative child care arrangements.
Germany has also banned large gatherings, and states are increasingly asking restaurants, bars, sports clubs and other public places to shut their doors as well.
Germany's islands in the North and Baltic Seas also closed themselves to tourists from Monday.
And Bavaria planned to declare a disaster situation to allow the state's authorities to push through new restrictions faster, including possibly asking the army for assistance.
German President Frank-Walter Steinmeier urged citizens to limit their social contacts.
“Restrictions on our lives today can save lives tomorrow,” he told the news site t-online.de.
“We will conquer this virus,” he added.
Germany has so far recorded 6,245 confirmed infections and 13 confirmed deaths. There have been 46 full recoveries.
'Limit border crossings to a minimum'
Chancellor Angela Merkel and Seehofer met with state premiers from affected German regions on Sunday to agree the closures, the newspaper claimed.
Paris, meanwhile, said the decision had been taken in coordination with the French government.
Yet the French Interior Ministry insisted that the border would not be fully closed.
“We are going to limit border crossings to the strict minimum, while allowing people and merchandise to go through. It's not a closure,” a ministry source told AFP.
While the German measures currently apply to five countries, other neighbouring countries such as Poland and the Czech Republic have also closed their borders or introduced severe restrictions.
Germany had until now resisted closing its borders so as not to endanger the Schengen agreement, which guarantees free travel between European countries and has already been put under strain in recent years by the migrant crisis and the threat of jihadist terrorism.
But with Europe now considered to be the epicentre of the pandemic, calls to close the border with France had begun to emerge shortly before Sunday's decision.
“The spread of the virus has to be slowed. The basic rule should be: anyone who doesn't urgently need to cross the border should not cross the border,” said Thomas Strobl, interior minister of Baden-Württemberg state, which borders France and Switzerland.