When picking up food, customers are asked to not open their car window until food is placed on a ledge outside by staff and the drive-through window to the restaurant is shut.
Unite Union national secretary John Crocker said the payment process was "frustrating".
"They've got a stick for eftpos or cash but in most situations, the customer and the worker are going to be in two metres of each other, which we think breaches the guidelines," Crocker said.
Other restaurant organisations such as Restaurant Brands, which runs KFC, Pizza Hut, Carl's Jr and Taco Bell, closed the window between staff and customers during payment, he said.
The Council of Trade Unions president Richard Wagstaff agreed it was a concern.
"That's a high-volume part of our economy, people going through drive-throughs, and the worst thing that could happen obviously is that we're spreading infection and the pandemic there."
McDonald's spokesperson Simon Kenny said unlike some other businesses, general security measures meant eftpos units were wired and secured, so completely closing a window was not possible.
"We have a number of additional controls in place to manage risk, including employee protection screens, increased use of protective equipment and enhanced hygiene and sanitation. We also have multiple points reiterating to customers that masks are required."
McDonald's had submitted its processes to WorkSafe, he said.
Crocker said he did not find McDonald's' argument "compelling".
He was trying to get WorkSafe to tell McDonald's the processes were not acceptable, but was having little luck.
"WorkSafe have agreed to something that we think is incorrect, now they're kind of softly agreeing with us, but not telling the company that they need to do the right thing.
"When we can't achieve what we want to through engagement with the company, we need a regulator that's going to back us up."
WorkSafe has been approached for comment.
- RNZ