The stores, including Marks & Spencer, Safeway and Tesco, and their importers could be prosecuted for the lapses, which were found in various types of pears, including Conference, William and Rocha.
Jeff Rooker, an agriculture minister, said there was no risk to health. But by naming the stores, the Government is clearly seeking to force the retailers and their importers to improve their own checks on pesticides in food.
A range of pesticide residues were found in small amounts, but ministers were alarmed to find traces of chlormequat, a growth regulator that can improve the size of pears.
Use of the chemical is banned in this country because the manufacturer has failed to supply information to the UK regulator, but it is allowed in other parts of the EU. Some of the traces were well above the doses permitted for chlormequat in EU countries.
Conference pears bought at a Marks & Spencer store in Wrexham were found to contain more than the permitted EU level; they were grown in the Netherlands. Lower levels of the pesticide were found in spot checks on Conference pears from the Netherlands at a Sainsbury store in Grimsby.
Mr Rooker said: "There is no health risk but this shows that stores and their importers need to take more care. The public ought to know that this policing work is going on so that they can feel confidence in the system of checks."
About 3,000 samples were taken by inspectors. Four out of five samples recorded as UK-grown contained detectable levels of chlormequat. The pesticide was detected in pears grown in Italy, South Africa and Spain. Pears grown in Belgium and sold at Somerfield in south-east London contained more than the EU maximum residue level.
The checks have resulted in a number of consignments of Dutch and Belgian pears being rejected by UK retailers. The Dutch and Belgian authorities have been warned. They have given assurances that a more rigorous screening programme for exports to Britain is being put in place.