Yes, it is safe to cook eggs in the microwave oven if you just follow the USDA recommended temperatures for microwaving food like eggs safely. Eggs and casseroles that contains eggs should be cook at a 160 deg. F.

Bacteria are destroyed during microwave cooks and so food is safely cooked in a microwave oven but the food can be unevenly cooked compared to a standard oven. Because of this reason it is a must to use a food thermometer and test food in several places to be sure it has reached its recommended temperature so that bacteria and other pathogens that can cause illness will be destroyed.

Cooking time varies fro different types of food:
These are the safe and USDA recommended cooking times and temperature when using a microwave oven:
Ground meat should be cooked at 160 deg. F while ground poultry up to 165 deg. F
Beef, veal and lamb steaks, roasts and chops should be cook to 145 deg. F and all cuts of fresh porkat 160 deg. F.
The minimum internal temperature of poultry should reach 165 deg. F
Fish cooked at 145 deg F

Hi there, @librarian!
My answer is a resounding no. Although microwave has been said to kill germs in food, it is still not safe to eat anything that is being heated and cooked in it. Talking about salmonella, yes, you maybe safe from it but you're not safe from the harmful effects which are brought about by microwave's harmful radiation. I still can remember about what I read in an article that said a study had found out that those who had eaten microwave-heated spaghetti had their hemoglobin significantly lowered. That is why I’ve come to a general idea that microwave is very dangerous and I should not allow my family to eat anything that’s heated or cooked in it as much as possible. In fact, if my kids would want to eat spaghetti or anything that needs to be heated, I would always request that it wouldn’t be heated anymore because I am carefully avoiding the harmful effects. Besides, it’s too expensive to be sick of cancer. When it comes to cooking eggs, you can always cook them well without the use of a microwave. I think I have focused more on microwave here and not on salmonella but I see that it’s important also to share any information that can be helpful to anyone.
“Cancer
Carcinogens are formed in virtually all foods tested. In scientific tests, no test food was subjected to more microwaving than necessary to accomplish the purpose of cooking, thawing or heating to insure sanitary ingestion. Microwaved foods caused stomach and intestinal cancerous growths, as well as a general degeneration of peripheral cellular tissues, with a gradual breakdown of the function of the digestive and execrative systems. There is a binding effect to radioactivity in the atmosphere, thus causing a marked increase in the amount of alpha and beta particle saturation in foods. There is a creation of cancer-causing agents within protein hydrolysate compounds in milk and cereal grains (unnatural proteins that are split into unnatural fragments by the addition of water). Microwaving prepared meats sufficiently, to insure sanitary ingestion, result in the formation of d-nitrosodienthanolamines, well-known carcinogens. Microwaving milk and cereal grains converted some of their amino acids into carcinogens. Thawing frozen fruits converted their glucoside(hydrolyzed dextrose) and galactoside (hydrolyzed alcohol) containing fractions into carcinogenic substances. Extremely short exposure of raw, cooked or frozen vegetables converted their plant alkaloids into carcinogens. Carcinogenic free radicals are formed within certain trace mineral molecular substances in microwaved plants, especially root vegetables. Due to chemical alterations within food substances, malfunctions are observed within the lymphatic systems causing a degeneration of the immune potentials of the body to protect against certain forms of neoplastics (abnormal growth of tissue). Microwaved foods cause a higher percentage of cancerous cells within the blood serum (cytomas--cell tumors such as sarcoma).”

Microwaves heat food by using microwave radiation to excite the water and fat molecules within the food. Those excited molecules then generate heat which in turn cooks the food. In that regard, microwave cooking should be equally effective at killing bacteria as any other type of cooking. The only requirement is that the food be heated to the appropriate temperature to kill the harmful bacteria (160 degrees Fahrenheit is a good guideline). In the case of eggs, I would cook them thoroughly so they yolk is not runny.

I’ve cooked eggs in my microwave for years as a way to make an occasional, homemade Egg McMuffin. By putting an egg in a small dish and cooking it in the microwave I can get the perfect shaped egg. In all my years of doing it, I’ve never had a problem with any of the eggs.