Although the team has previously stated its intention to always run a Chinese driver, Ma and members of the Lisheng Racing-owned team based in Shanghai will be unable to attend the three double-header events at the Tempelhof Airport in Berlin.
The country's capital city of Beijing is currently battling a fresh outbreak of the virus, leading to wider domestic and international flight restrictions.
Ma said: "Unfortunately, I am not going to Berlin this year, having raced there during the 2015-16 season.
"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 discussion about this, and considering the current situation of the pandemic, this decision was made to ensure the best possible preparation for the team."
Ma - who is currently last in the FE standings - is expected to continue at the team for the following 2020-21 season, which features the return of the Sanya E-Prix in China.
Of the five races held so far this season, Ma crashed out of the Mexico City E-Prix and finished last on the road in both Diriyah events and in the most recent Marrakech race.
Vincent Wang, the team CEO, added: "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."
It is expected that former Audi driver Daniel Abt, who was effectively sacked by the team when he had a sim racer take his place in the FE Race at Home Challenge Esports series, will deputise for Ma.
NIO 333 teammate Oliver Turvey is 21st in the points, notably having progressed through to the superpole qualifying shootout in Santiago.