An orange crawling with maggots was also found during the regular checks made on the hundreds of outlets, from carry-outs to restaurants, in Glasgow
Duncan Scott is assistant manager of Glasgow Scientific Services - the biggest public analyst laboratory in the UK.
He made the grim rodent discovery while checking the contents of a meal from an un-named restaurant.
Mr Scott said: "You could still see the hairs on the paw.
"I just had to wonder what happened to the rest of the mouse..."
His colleague Jane White also made a stomach-churning find while checking out an orange.
She said: "I cut it in half and it looked perfectly normal."
Ms White got on with other things but when she returned to the fruit she discovered it was packed full of maggots which had turned the same colour as the orange.
She said: "They had started crawling out of the orange onto the work surface."
Team members have also found frogs in salads, lizards in tins of fruit, a potentially deadly black widow spider in a bunch of grapes and nuts and bolts in meals.
Most of the checks carried out by the highly experienced city council team are less dramatic.
At present, they are doing routine analysis of fish suppers bought across the city.
Ms White said: "We go out and take survey samples where the chip shop claims to be selling haddock and cod.
"The majority is what it claims to be but we have also found a variety of other fish - for example, whiting being sold as more expensive cod."
Gary Walker is scientific and regulations services manager for the unit, which provides a testing service for 16 of Scotland's 32 local councils.
He said: "One of the things we do is look at fish and meat substitutes.
"Samples come in to here, are tested and we produce a report based on our evidence.
"If it is claimed the fish is haddock, and we find it is whiting, a report goes back to environmental health officers and they will follow it up with the shop."
One recent issue was the discovery that some Indian restaurants and kebab shops in the West of Scotland were substituting lamb for beef.
Glasgow Scientific Services staff have also recently been checking food sold by shops and vans based within a one mile radius of schools.
They found some children opting not to eat balanced school meals but instead choosing to buy 'munchie boxes' from local fast-food shops.
The boxes, usually the size of a 9in pizza box, and are filled with naan bread, donor kebab meat, chips, veggie pakoras, cheese and sauce.
An analysis found the food in the boxes contained a staggering 5000 calories - around 10 times more than a child should eat.
And that does not include the can of juice and cake which comes with the gut- busting lunchtime meal deal.
Mr Walker said: "It is hardly surprising there is an obesity crisis in the West of Scotland."
Another favourite with pupils turned out to be a 'pizza crunch' - a pizza dipped in batter and deep fried.
Analysis has proved food is not always what it seems.
For example, the ham on some pizzas has been found to be reconstituted turkey, and beef burgers have turned out to be made of chicken.
Glasgow Scientific Services has been working with schools in a bid to get pupils interested in what is in their food and in science as a career.
And it has taken on a number of young people under the council's Commonwealth Apprenticeship scheme who are now pursuing a career at the Springburn laboratory.