"During these special times and circumstances, we must not let these people fall through the cracks," he added.
The program is for people booked to fly from April 23 to August 11 who arrived at Schiphol on time but missed their flight because they were stuck in a queue. It covers costs including rebooking a flight or booking a replacement flight, extra travel costs and accommodation, transport and activities booked at the travellers' destination.
Schiphol did not say how much the compensation program would cost the airport.
The Dutch Consumers' Association welcomed the plan.
"We investigated the possibility of a mass claim and then entered into discussions with Schiphol. Our joint efforts have resulted in this arrangement, which has helped a large group of consumers," association director Sandra Molenaar said in a statement on Schiphol's website.
Heathrow said Thursday that its cap on the daily number of departing passengers has eased the travel crunch at Britain's largest airport. It apologized last month to passengers whose travels were disrupted by staff shortages.