Simon Niepmann and Lucas Tramer won gold in South Korea in 2013 but they struggled on a rainy day in Amsterdam and finished back in third place in their heat.
The duo led for most of the race but saw their lead disappear in the final 200 metres as Ireland and China claimed the automatic semi-final places on Monday.
They will be joined by heat winners Great Britain and France, while Czech Republic and the Netherlands also qualified.
In the Men's Coxed Pairs there was more disappointment for defending champions, as Italy were forced into the repechage when Great Britain beat them in heat one, with New Zealand the only other boat guaranteed a final place.
Greece had no such problems as they strive to retain their Lightweight Men's Quadruple Sculls title, cruising through their heat to reach the final.
They will be joined by Germany, who won heat one, China and Italy.
In the women's event the home crowd were given something to cheer as the hosts booked their final spot along with Germany, Italy and Australia.
Italy were the only 2013 medalists to book a semi-final berth in the Men's Double Sculls as Croatia, Germany and New Zealand won the other three heats.
That leaves defending champions Norway and silver medalists Lithuania to battle it out in the repechage along with Great Britain, who were narrowly beaten by Germany in their heat.
Lithuania began their defence of the women's event in style to claim their heat and book a semi-final place and they will be joined by China, Australia and Poland - who took first place in the other three races.
Denmark, Australia and Great Britain progressed to the semi-finals in the Lightweight Men's Four by winning their heats, with runners-up places for France, New Zealand and the home nation
The Women's Four was dominated by New Zealand and the United States, while Germany and Poland took heat wins in the Men's Eight.
In the Lightweight Men's Single Sculls repechage Slovakia, Algeria, Great Britain and Peru moved into quarter-finals, as did Russia, Hungary, China and Mexico in the repechage of the Lightweight Men's Double Sculls.
The repechage's of the Single Sculls events saw Croatia, Slovenia, Argentina, Spain, Romania and Switzerland qualify in the men's race, while Zimbabwe, Hungary, Denmark and Argentina will be in the women's quarter-finals.