The Conservative Cabinet Minister told the Trussell Trust he denied claims that benefits reforms were linked to the rocketing number of people turning to it for help and suggested the organisation was political.
Since April more than 500,000 people, of which one third are children, have received emergency supplies from the 400 food banks run by the Trussell Trust charity. Food parcels are expected to be handed out to more than 2000 people in Scotland over the two-week festive period.
The Trust has asked on a number of occasions for meetings with DWP ministers.
But Mr Duncan Smith wrote:"I strongly refute this claim and would politely ask you to stop scaremongering in this way.
"I understand that a feature of your business model must require you to continuously achieve publicity, but I'm concerned that you are now seeking to do this by making your political opposition to welfare reform overtly clear."
Lord Freud, the minister for welfare reform, also turned down a request.
Trust chairman Chris Mould said: "We are deeply disappointed, but we are as open as ever to meet ministers in the hope that perhaps the new year will bring a fresh approach to what could so easily have been a fruitful dialogue."
A DWP spokeswoman said: "There is no robust evidence that welfare reforms are linked to increased use of food banks.