Tagging the flippers of penguins for long-term scientific studies significantly limits their chances of survival and ability to raise chicks, according to a decade-long study in the Antarctic.

The researchers found that the survival rates for king penguins with flipper bands dropped by 16% and the birds produced 39% fewer chicks. The finding raises serious questions about the ethics of banding penguins for research and casts doubt on years of data produced by tagging the birds in this way.

Flipper banding, a technique that involves placing a band usually made of stainless steel under penguins' flippers to identify them, is used by some researchers to identify them and gather long-term information about their behaviour and ecology.

The latest available figures, from a study published in 2000, show that between 1988 and 1996, 36,000 penguins were flipper banded by scientists.

The study, published today by French researchers in Nature, followed 100 penguins over 10 years, half of them with the bands and half without.

"At the end of the study we had much higher numbers of non-banded than banded birds," said Claire Saraux, at the University of Strasbourg who co-authored the study.

Bands also heavily impacted the birds' breeding success. "Banded birds would arrive later at the colony to breed and so they would begin breeding later. Our idea is because of the drag effect, they spend more time at sea and it takes them longer to swim back to the colony, so they are at a disadvantage," said Saraux.

The drag effect of the bands means the penguins swim slower and expend more energy than they otherwise would. In 1994, Prof Rory Wilson of Swansea University conducted a study which found that penguins with flipper bands used 24% more energy to swim.

The authors of the report say that while tracking penguins is essential to understanding changes in their population and the effects of various factors including rises in sea temperatures, flipper banding is problematic because it may distort the results.

"As we show in our paper there is a drop in breeding success and it is known in sea birds that when this fails it induces immigration to other colonies so then there is a problem if you use flipper banding to study immigration. It will skew the numbers," said Yvon Le Maho, the report's lead author.

To track the non-banded birds in their study, Le Maho and Saraux used tiny electronic chips with radio transmissions. Le Maho says this is a possible alternative to flipper bands but that it presents other challenges.

"The only difficulty is that once a bird is only with an electronic tag you need an antenna for identification – so to study immigration you need antennas in different colonies – you cannot do it simply by observation as you do with flipper bands but again [flipper bands] skew the data," he said.

Wilson, who has been studying penguins for three decades, said: "The big question is does what you get from the study justify the cost – and the costs are increased mortality without a shadow of a doubt and decreased reproductive success."

"It is going to be very difficult as a scientist to come back and defend flipper banding and the hope is that if people don't stop flipper banding they're at least cognisant of what it implicates," he said.

Wilson says although the practice has been in decline in recent years, there is no comprehensive ban or policy against it internationally.