Usually, this is caused by poor water quality with possibly a high ammonia content, or it could be  Ich or Flukes that may be infesting the gills

You should be aware that Fry do not handle ANY ammonia accumulation or other water quality disorders.

I may recommend the use of Salt... It's safe for fry.

If the water quality seems to be Ok then there is the likelihood of gill flukes if the tank, or pond that the fry are kept in is in the open air .. but this then also causes a problem as it is impossible to treat the pond to eradicate the flukes as young fry cannot withstand the treatments which would be needed to eradicate the flukes - so there is very little you can do other than use a salt solution at 5% to 7.5% (1 ounce to 1.5 ounces per gallon) this may help kill off the flukes and should not harm the fry.. it is worth a try ...