Dr Clark disagreed with the arrangement in which which some small DHBs, such as Northland, have been forced to pay as much as $70 million a year.
"It has to be considered in base funding," he said.
He said the current system particularly disadvantaged smaller health boards, which also have administration costs associated with the payments.
In February, Whanganui DHB corporate manager Brian Walden said the price of local patients' treatment outside the region was an issue for the board.
"There's a $35 million flow into other district health boards - as our patients go out to other care, the money follows them," he said.
"So when these patients go down to Capital Coast or to Starship Hospital, we are funding those places, and often those costs are quite considerable."
The country's 20 health boards agreed on a national price for services, but some regions had a much larger number of patients receiving treatment in other areas.
In return, the Whanganui DHB received just $7 million from other health boards in the last financial year.
Julie Patterson, Whanganui DHB's chief executive, said the board was further likely to be missing out on some revenue due to patients from outside the area not giving their home addresses.
The payments to other region's DHBs have been significant outlay for the board, which had an annual budget of approximately $230 million.
