I replaced the ignition switch module on my 2003 honda civic and now the immobilization system will not let the car start it will crank but thats all I tried turning the key on to the full on position and leaving it on for over 25 mins and the green key icon on the dash stayed flashing the whole time so apparently that solution doesn't work on hondas or I'm doing something wrong is there any way to reprogram the new ignition module to the car without having to get it towed to a dealer and costing an arm and a leg? Help!

not told does engine crank fast. keyed to crank.????
yes / no . if not say that first.
the starter motor in a car is the best battery tester there is. so is starter dead./????????????
the IMMO on 90%of cars cuts fuel dead onlyl.
on the 10% it cuts starter and fuel both dead
many allow engine to run for 1 to10 seconds and stalls
the IMMo can not be hacked, and is its A#1 top designed purpose to do that, to stop thieves dead.
and works. all new cars have it and is mostly now mandated by laws.
this car I think cranks if key is bad. but will not start

all cars came with it new 2 new keys,working
lost the 2nd.?
we spend a huge amount of time here reading users guides to people lost. the manual is free to read.
at any time , im reading yours now google found it is 1second flat and 1st hit.
my posts are for USA cars only, nothing else ever.
unless they beg, LOL
the immo lamp is in the hot cold, fuel gauge port
if the IP cluster
i see a KEY icon there.it says read page 67
so I do.

"This indicator comes on for a few
seconds when you turn the ignition
switch ON (II). It will then go off if
you have inserted a properly-coded
ignition key. If it is not a properly-
coded key, the indicator will blink
and the engine will not start (see
page 81"
shows 2 immo keys and 1 valet key new

"If an improperly- coded key (or other device) is used,
the engine's fuel system is disabled
When you turn the ignition switch to
ON (II), the Immobilizer System
indicator should come on for a few
seconds, then go out. If the indicator
starts to blink, it means the system
does not recognize the coding of the
key. Turn the ignition switch to
LOCK (0), remove the key, reinsert
it, and turn the switch to ON (II)
again."

do not have other immo keys near the ignition switch
just 1 honda immo only, not even other cars IMMO keys.near, (as the manual said) and is true.
or the keys go to a loggerheads war (radio signals clash)

free guide

https://www.manualslib.com/manual/832826/Honda-2003-Civic.html?page=81#manual

Sounds like the immobilizer is shutting down the fuel pump. Make sure any ignition/key is programmed to the car. There are issues with the immobilizer in these cars also, so you can visit some Civic forums to read further.

You can't start this model without the correct key due to the anti theft immobilizer system. Older models (pre96) could be hotwired or a screwdriver to the ignition switch, but not possible on these it newer.

They check the immobilizer system? Also ignition switches fail.

By "won't fully turn over," do you mean it cranks slowly, or that it cranks normally (fast), but won't start? Does it even stutter, as if it is trying to start, or does it simply crank and crank with no change in the sound? If I am interpreting what you said correctly, then you may simply have drained the battery, and now it is turning over too slowly to actually get the car to start. If possible, get someone qualified to jump start it and see if that works. If so, then you will need to have the battery re-charged, or at worst replace it. I hope it turns out to be simple/low cost.

sound like problem could be clutch start switch.or your new engine need to be reprogrammed to the ignition switch immobilizer module and ecm.

If it were the immobilizer, you would have a security light that would be flashing or staying on all the time the key is in on. Since the engine cranks over and the pump is working when you turn the key to on and start, the green light may just mean the bulb is burnt out or a connection problem with that wire for the light. Not much of a problem there.
You said no fuel or fire when trying to start-so that is where to concentrate: you first need to verify that the ignition still is working, so check for spark on a plug wire with the engine cranking over. This could be a main fuse or main relay not passing power on to the ignition system and/or the injector circuit. First check for spark, and if you have spark, check the injector circuit (there is a fuse for the injectors-probably under the hood in a fuse/relay block). If you have no spark, you will have to diagnose the ignition system- coils, ignition control module (the ignitor), the crank angle or crank position sensor, finally the engine computer.

LOOK FOR A 15 AMP IGNITION FUSE UNDER THE LEFT DRIVER SIDE OF THE INSTRUMENT PANEL.IF FUSE GOOD YOU HAVE A BAD COIL OR FAULTY IGNITION CONTROL MODULE.

That's your immobilizer system light:
The Immobilizer System protects your car from theft. A properly coded master or valet key must be used in the ignition switch for the engine to start.
If an improperly coded key (or other device) is used, the engine’s fuel system is disabled.
When you turn the ignition switch to ON (II), the Immobilizer System indicator should come on for a few seconds, then go out. If the indicator starts to blink, it means the system does not recognize the coding of the key. Turn the ignition switch to LOCK (0), remove the key, reinsert it, and turn the switch to ON (II) again.
The system may not recognize your key’s coding if another immobilizer key or other metal object is near the ignition switch when you insert the key. To make sure the system recognizes the key code:
Do not keep other immobilizer keys on the same key ring.
Use a plastic or leather key fob, not metal.
Keep other keys away from your vehicle’s key and the ignition switch while trying to start the engine.
Do not attempt to alter this system or add other devices to it. Electrical problems could result that may make your car undriveable.
This indicator will also blink several times when you turn the ignition switch from ON (II) to ACCESSORY (I) or LOCK (0).
If the system repeatedly does not recognize the coding of your key, contact your Honda dealer.
If you have lost your key and you cannot start the engine, contact your Honda dealer.
Hope this lets you understand the light, and what should be happening.

Its the electrical part of the ignition switch.. thats pretty common for a 91 Honda