The news comes after Dutch single scull competitor Finn Florijn, 21, tested positive on Friday.
Another staff member of the Dutch rowing team, along with Dutch taekwondo competitor Reshmie Oogink and snowboarder Candy Jacobs, tested positive last week.
Verdonkschot is the head coach of “several” women’s boats competing in the Tokyo Games, but has not traveled with the four members of the Netherlands squad who have tested positive, TeamNL said.
“My personal feelings don’t play a role,” Verdonkschot said in a written statement.
“Our agenda is well put together, we know each other what we can and must do. The absence of the coach no longer has any influence. My confidence in my staff and my athletes is infinite. They will finish this job.
Some 132 people accredited to the Tokyo Games have tested positive for COVID since July 1, according to organizers.
TeamNL said Verdonkschot had been briefed on his Saturday morning test results that evening and was following all close contacts under the Tokyo 2020 guidelines.
Close contacts will be allowed to continue competition “under special conditions”, including taking separate transportation and eating and sleeping in separate rooms.
“He is fine, we got a message from him and he looked relaxed and confident,” said Dutch rower Sophie Souwer, who progressed in the single scull after finishing second in her quarter-final.
“We were already sharp from the start, now we are even sharper. We have a lot of coaches around us and people who are always on the course and around us.
The Dutch dominated at all levels in the first competitions of the Sea Forest Waterway and four boats were scheduled to compete on Sunday.
The Netherlands won three rowing medals at the Rio 2016 Games.