He was replying to a question from Otago District Health Board chairman Richard Thomson regarding the funding of Herceptin for women with Her-2 positive breast cancer.
There has been controversy over Pharmac's decision to fund a nine-week rather than a 12-month course of the drug .
Mr Waddel told Mr Thomson it would cost $20 million extra a year to fund the 12-month course.
When Pharmac was considering the issue, it received submissions from two significant women's groups which did not support the 12-month treatment because they feared there were other areas which would miss out.
The nine-week decision was based on available evidence suggesting the benefits of that were similar to the 12-month treatment but without the side effects.
He said he felt very sorry for women with Her 2 positive cancer, and could understand their point of view.
Pharmac could not be directed to fund drugs by politicians.
Mr Thomson said that seemed to have been "lost in translation" in the last few weeks.
(The National Party has said it would fund a 12-month Herceptin treatment outside the Pharmac process, spending an extra $9 million a year for three years.)
Pharmac chief executive Matthew Brougham told the board 40 new cancer drugs were expected to become available internationally in the next two or three years, and many were expensive.
In the United Kingdom, it had been estimated that if all were to be funded publicly, tax there would have to rise by 60%.
He pointed out that new drugs of any description were not necessarily better overall than old medicines, although some people might respond well to them.
Some new drugs also had more significant side effects than some of the older ones.
Mr Waddel, during his presentation to the board, said he did not believe proper use was made of pharmacists who were highly skilled, highly trained health professionals.
They were given a fee for dispensing medicine, but they did not get rewarded for other things they did or could do in their face-to-face contact with patients.
Pharmac would be interested in conducting research into the outcomes of its decisions.
If it made a major decision on a medicine, based on evidence available at the time, it would be useful to find out two years later whether the expected benefits resulted.
The organisation might need to pursue that harder, something which would require funding.
