Is it okay to continue to work for a (non-defense) federal government agency under an administration hostile to my own moral and ethical beliefs?

I’d say it’s more important than ever. Leaving just allows the “yes” men to get more power and gives more control to the regime you dislike/disagree with.

Resist

Yes it is - you can continue to do good in the ways you can manage.

I work for the USPS. We took an oath to the constitution and it's very easy to understand why. The Postal Service is a necessary component of democracy as long as it remains true to what its supposed to be, which is a pipeline of information between any two points in the world. We can debate the legitimacy of that need after the internet, but there are vital services the USPS provides that the internet can't.

I don't like the direction things are going, but i still want to be a part of that. All i can do is make sure the mail I get is getting where it's supposed to be.

If you believe in what you do and that's important to you, then stick it out. If it's not, then that's fine, but you may want to get out for your mental health.

The resistance infiltrating the enemy base in disguise can get a lot of work done. Especially if it's long term and you don't even need to sneak around.

Even just a low level functionary who's not a nazi or a terrible person makes my time dealing with a government agency better. There's not an automatic moral imperative to bounce.

You work for the government, not for whatever yoyo happens to be President at any given time. You wouldn't necessarily leave a private sector job if the CEO changed.

OTOH, this administration has been making a point of wanting to make government so small they can drown it in the bathtub. Unless you work in one of the very few Project 2025 priorities, they will probably eliminate your job eventually. So keep a keen eye out for alternatives.

Working for the agency isn't the problem on its own. If your job requires you to do something that is against your morals, resist up to and including loudly leaving that job if that's what's required. But until then it's more important than ever to stick it out and push to make things better any way you can.

So assuming you're an American. I hate to break it to you but your government has done way worse stuff than elect an orange guy. I seriously doubt everything done holds up to the slightest scrutiny to your moral and ethical code. The only difference is now you are aware of it. If it was me I would ask myself if I felt guilty for the work I had done already. If I did I would stop if not I wouldn't.

A few months ago a german activist (I think it was Arne Semsrot) wrote a book about how low and middle positions in government agencies can work against the governments intentions in case of a extreme right wing takeover by the AFD. Though I don't know, if it was translated to english or would be 1 to 1 applicable to the USA.

The answers to both of your questions are probably yes it's okay, and yes you should probably be looking for another job.
Are you morally/ethically okay with your agency's mission? With your role in it? If you are, then the new administration's policies may not be reason enough to leave. You pretty much have to work somewhere. If the answer is no, you probably would have already been looking for another job.
Should you be looking for another job? Probably, depending on what your agency is and it's mission. If TFG and Project2025 have their way, many federal government agencies will be defunded and/or privatized, and pretty much toothless when it comes to enforcement. We already saw what happened to the EPA under the first Trump administration. If yours is in danger of that you should be preparing a backup plan. I wouldn't want to give up a government job, but I would want to be ready if I got RIF'd, or if I got fed up with the bullshit.

Do you feel that your “customers” are the administration or the general public? Whom do you feel that you are serving in your job? Do you feel that the directions given to you by your administration are legal and safe and reasonable? Do you feel that the directions given to you by your administration cause a disadvantage to yourself or your “customers”?

You could try to clutch at straws to justify staying in your job. You might be able to reasonably determine that your feelings for your administration don’t affect the performance of your job. Maybe staying in your job is the best way to benefit your “customers” and obstruct the administration.

Only you can decide how you feel and what is an appropriate match for your own moral and ethical position.

If you quit another will take your place. Possibly a conservative. You'd do more good holding that seat than giving it up.

We need people like you to resist when you feel like it’s the right thing to do. You took an oath to protect and defend the Constitution from enemies foreign and domestic. As cringe as it may sound, we need you and others like you to do that now more than ever…because there is an obvious threat.

Dude, if you quit, a Maga is taking your place. The last thing we need is more extremist infiltration of the government.

Stay, we need you. Your country needs you.

If there is any shady things happenning, we need you to be a whisleblower.

Yes.

Schindler couldn't do it alone.

Of course, as long as the work you do doesn't become hostile to your own beliefs. I mean, people that process social security still provide benefits to millions of people no matter who is in charge, at least until Republicans destroy it.

Yup. Watch The Good Place, then ask again.

What is the difference between a rebel and a revolutionary?

See if you can gum up the works, and if you feel yourself changing, get out.

At the very least, make them fire you. Don't quit.

I know this is cliche as hell, but only you are going to be familiar enough with your position to be able to know if you can effect change, prevent harm, or if your labor won't be able to do much but perpetuate things you stand against. Id wager it wouldn't happen all at once, but eventually you may see a red line you don't want to cross. Use the time you have now to keep an eye out for a job listing that looks like a Cinderella slipper, and if you start seeing that red line coming up before that happens, then start to seriously consider whatever offers you can find that seem workable to you.

Unfortunately, thatt's a question only you can answer. But goes without saying for any job.

Ask yourself:

• Will you be able to sleep peacefully at night knowing what job you're doing and who you're doing it for?
• Are your morals stronger then job security you're getting?
• Can you stay on the job and inact change from within?
• Can you refuse certain tasks you don't feel conformable with?
• Can you steer / influence the work that you and/or the agency does?

If administration does not change agency’s policy in the the way it contradicts your moral I’d say it’s ok

If you're working for the government, you had no morals and integrity before.

No quit

No one can answer that question but you.

Maybe you should leave the country if it upsets you that much