The European Food Safety Authority (EFSA) said these samples came from eight countries with most from the Netherlands.
The agency recommended fipronil be included in future monitoring by member states.
Results come from a monitoring programme put in place after widespread detection of fipronil residues in eggs last summer. Fipronil is an insecticide and cannot be used for animals intended for the food chain.
It was found in Dutch and Belgian farms and millions of eggs were withdrawn from the market.
The European Commission Maximum Residue Level (MRL) for fipronil in eggs and poultry meat is 0.005 mg/kg (5μg/kg). Levels up to 1.2 mg/kg were detected in chicken eggs and meat in Belgium.
The World Health Organization (WHO) has classed it as "moderately toxic" if consumed in large quantities.
Chicken eggs most affected
Member States provided results for 5,439 samples of eggs and chicken muscle/fat which were analysed for fipronil and other active substances proposed by the European Commission in view of potential misuse in poultry farms against red mites.
Analysis showed 742 of them collected between September and November 2017 contained residues in quantities exceeding legal limits.
These came from the Netherlands (664 samples), Italy (40), Germany (13), Poland (11), Hungary (six), France (five), Slovenia (two) and Greece (one). Malta, Lithuania and Sweden did not provide data.
Food affected was mainly chicken eggs (including products of egg yolk and white) and fat of laying hens.
Quantifiable residues were most frequently in chicken eggs (467 samples) produced in the Netherlands, followed by fat of laying hens (184 samples) from the same country.
Among 2,540 suspect samples, 574 contained residues above the legal limit. For the 2,899 random samples, 168 exceeded the limit.
Samples above the MRL were mostly fipronil with unprocessed chicken eggs (601 samples), fat of laying hens (134), muscle of laying hens (five) as well as dried egg powder (two).
Fipronil and amitraz
In Germany, authorities collected 2,149 samples under the programme with 16,672 analysis results. Fipronil residues were detected in 8% of them but none exceeded levels considered by the Federal Institute for Risk Assessment (BfR) as potentially harmful to health.
Among the 66 substances recommended to be analysed, the only ones found in quantifiable concentrations were fipronil (915 determinations) and amitraz (two).
In one sample of chicken eggs produced in Italy (random sampling) the MRL was exceeded for amitraz residues.
Eleven acaricides were included in the monitoring programme: amitraz, bifenthrin, cypermethrin, diazinon, etoxazole, flufenoxuron, ivermectin, pyridaben, pyriproxyfen, thiamethoxam and trichlorfon.
Only a small amount of samples related to production according to principles of organic farming (374 of 5,439); the others were related to conventional production.
Nine samples produced in third countries (US, Ukraine and Brazil) and 350 items made in one EU Member State but analysed by another were reported.