Honda civic 2004: the car alarm (factory installed) goes off when we unlick the car with a key, but not with the remote. How do we stop the car alarm from going off?

What year is this? Is this a factory OEM system?

Try this relearn procedure for Honda key fobs.
Cheers!

Here are the options for disarming a factory alarm while it's going off:

1. Close all doors, trunk and hood. Alarm will stop after preset time.

2. Hit the unlock or lock button on the remote. (One of the 2 works... I just don't remember which.)

3. With all doors, trunk and hood close, insert the key in the driver's door and unlock/lock the doors manually.

Also, is it a factory security system? Is it a honda key fob? or a remote start system perhaps?

Try locking and unlocking the doors with the key to see if it will reset the security system.
It is possible a relay could cause this...there are many relays and computers in this hybrid system

Unlock the drivers door twice. The other doors have to be closed and if their not electrically closed it'll still not reset. Double lock the drivers door with the key all the doors should lock.. The alarm should stop. Unlock the drivers door and then get inthe car and start it soon. the sysstem should go though a full reset and it should be normal again.

There is most likely a reset button under the dash somewhere. You can try pressing and holding that button down while pressing the lock button on the remote. If this does not work simply have the dealer reset it for you.

If you hook up the jumper cables can you disable the alarm with the remote?

I had this happen today and called an alarm installer. he said to connect the battery cable (id unhooked it to stop the blaring) then open the door to set off the alarm. then torn on the key ( even tho it wont start the car , turn it on anyway) then look for a toggle switch ( AKA a valet switch) with the key in the on position flip the switch. ( when I did this a noticed a tiny red light come on to the left of the steering column) I turned the toggle back to the original position and then I tried to crank -AND IT CRANKED WITH NO SCREAMING ALARM!!! I was so happy, I had to post this in case it could help someone else.

Hi Nina, what year is the car? we need to Identify if this is a factory fit or a retrofit alarm. Once I know that I may be able to help.