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The current restrictions would have affected Ma's arrival into Europe for the three double-headers in Berlin but also his subsequent re-entry back into China.
"Unfortunately, I am not going to Berlin this year, having raced there during the 2015-2016 season," said Ma. "It is quite difficult to travel and race abroad at present, as this would expose us to more Covid-19 risks.
"The team and I had in depth discussions about this, and considering the current situation of the pandemic, this decision was made to ensure the best possible preparation for the team. I look forward to coming back and racing in the Season 7 World Championship."
Ma's return to Formula E has not yielded any points for the Chinese driver, having crashed out of the Mexico City race and three last-place finishes in both the Diriyah rounds and last time out in Marrakesh.
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The same travel restrictions will also mean that any Chinese-based team members will also be absent from the six races in Berlin. NIO 333 team CEO, Vincent Wang added: "We have certainly experienced some ups and downs during the first season of the regrouped NIO 333 FE team. When the plan to resume the championship was announced, we were all very excited to return, the long pause of the season made us miss the battles on the track, especially with the team making significant progress since Marrakech.
"However, due to the number of restrictions, Ma and the Shanghai team members, will be unable to attend the race. It is quite unfortunate, but we will continue to assist remotely. Ma will also be present during the live event with our fans as well as providing support to the team on-site. The management team is currently selecting the replacement for Ma, and an announcement will be made imminently."
Ma's replacement for the remaining races of the 2019/20 season is due to be announced by NIO 333 soon.