The quarantine measures come as the southern state of Bavaria announced a "free test offensive", while Berlin has begun issuing fines for mask avoiders for the first time.
With the summer holiday season kicking off across Germany, some states have begun implementing bans and quarantines for people arriving from heavily-affected regions.
In most states, travellers from the town of Gütersloh in North Rhine Westphalia must be quarantined for two weeks on arrival or show evidence of a negative coronavirus test in order to enter.
Gütersloh, along with neighbouring Rheda-Wiedenbrück and Warendorf, have all been placed under lockdown due to serious coronavirus outbreaks at meat processing plants in the region.
In addition, accommodation providers in Mecklenburg-Western Pomerania, Baden-Württemberg, Bavaria and Lower Saxony have banned travellers from high-risk areas – regardless of evidence of a negative test – while in some cases holiday makers from these regions have been asked to leave.
Mecklenburg-Western Pomerania's Prime Minister Manuela Schwesig confirmed to German broadcaster ZDF that vacationers from Gütersloh had been told to return home.
Ms Schwesig said that while her state’s "safe tourism" policy was strict, it has “been well received both by tourists and by locals”.
North Rhine Westphalia's Prime Minister Armin Laschet said he welcomed the restrictions – even though they were primarily directed against travellers from his own state - but emphasised that people from certain regions should not become stigmatised in the battle against the virus.
“The effort was worthwhile. It's a good thing that we now have common regulations in all states for how we combine risk prevention and freedom from travel,” he said.
“The insecurity and stigmatisation among travellers from Gütersloh in the past few days must not be repeated. We can only defeat corona together, not [fighting] against each other.”
Meanwhile, Germany's second-largest state of Bavaria has announced plans to make coronavirus testing free for all of its 13 million residents, regardless of whether or not they have symptoms.
Bavaria has been one of the hardest hit by the virus, with a number of new outbreaks in recent weeks.
State health minister Melanie Huml said on Sunday that “all citizens of Bavaria will therefore be promptly offered to be tested with or without symptoms by a resident contract doctor” in a massive expansion of the testing regime.
The state will cover the costs unless they are already covered by health insurance providers.
Ms Huml said the goal was “to prevent major outbreaks like that in Gütersloh”.
And in Berlin, police on Saturday announced fines of between 50 and 500 euros for anyone not wearing masks on public transport – two months after the requirement was first implemented.
Police said the fines were motivated by increasing non-compliance with the requirement in Germany’s largest city, where masks are also required in all supermarkets and retail stores.
A spokesperson for the Berlin transit network, BVG, said they welcomed police involvement as transit workers “do not have the authority to sanction violations of state regulations.”
The spokesman said approximately 25 percent of the three million daily passengers were not adhering to the mask requirement.
Despite escaping the worst of the virus during its initial spread, Berlin has seen several outbreaks in recent weeks amid fears of complacency among the city’s four million residents.