Old post response but a new fix for this to try...

My father has an 05 Civic 1.6 (so factory fit alarm) which was plagued with this problem as he is a low mileage user and despite my pleas to use the car more he kept taking more out of the battery than it had in it, hence many flat batteries...

First time tha battery went flat we had this problem.

A lot of forums came up with random turning the manual keys in locks so many times and in certain patterns etc to resert the alarm but none of them worked for us.

More digging on forums and it appeared the power sounder in the boot fails due to internal battery failure on the unit causing these symptoms. This seems to be well documented on various forums as a common Civic problem. So Honda had it in and the power sounder had (according to them) indeed ailed due to internal battery failure. £700 later a new power sounder was fitted and all was apparently well. This seems to be well documented on various forums as a common Civic problem. HOWEVER...

The battery went flat again a few months later and we had the same problem again - exactly like yours. Honda had it in (angry words exchanged re previous £700 repair) and after having it all day, said they had 'reset' it somehow.

A a couple of weeks later, another flat battery and the power sounder going off again. Telephoning Honda they were reluctant to reveal their secrets but I got a bit of info out of them and managed to guess the rest,

Try this, it worked for me and I haven't seen it documented anywhere else. If I get time and can be bothered to get user names and passwords I'll try and put it on some other sites as it's driven me mad!

Procedure...

1. Reconnect a fully charged battery. As the sounder kicks off as soon as you connect it I suggest you do up the positive terminal tight but just push on the negative terminal - if it wedged on it's enough, you can do it up later (just in case you need to disconnect it again when the noise of the alarm sends you insane).

2. Shut the bonnet fully (it has a microswitch in it that needs to 'know' the bonnet is shut).

3. Jump in the car and shut the door.

4. Put the key in and switch it to position 2 (all the light on, but engine off. Leave it there for a couple of seconds.

5. Turn the key off and remove it from the ignition.

6. Hit the lock button. The alarm should shut up and the doors lock. Hit the unlock button (doors unlock), then the lock button, then the unlock button again. I'm sure I did 2 lots but it might have been three.

7. Put the key back in the ignition but don't turn it yet, hopefully the back lighting will come on. Wait a couple of seconds.

8. Take a deep breath and turn the key... and with luck it should start with no alarm shrieking.

9 With the engine left running, pop the bonnet and tighten up the negative terminal on the battery. I did it this way as there was no way I was risking accidentally breaking the connection and having to do the reset process all over again! Just don't go near the positive terminal with the spanner!

10. Shut the bonnet. Turn off the car, jump out and lock it. Then unlock with the remote and jump in and start the car. All should be good.

This worked for me.

Which begs the question was there anything wrong with the power sounder batteries in the first place?

A tip for anyone who has flat battery + the alarm goes off after battery disconnected. Model Civic SE 1.4 2004

I had the issue this morning. When I connected fully charged battery the siren started sounding off. The issue has been solved after spending half a day in the car.

1. Disconnect the battery
2. Make sure all the doors in the car are closed and open a bonnet
3. Lock the driver's door with the key from outside
4. Connect the battery and shut the bonnet fully (the alarm will start sounding off)
5. Unlock the drivers door with the key from outside (the siren will stop). Lock it again with the key. Then lock and unlock it again.
6. Turn the engine on