An obscure movie featuring a mysterious amphibious monster I remember very little detail of this movie that randomly aired on TV about a decade ago. Here is what I do remember:


Dark overtones reminiscent of future noir style. The animation, similarly, is reminiscent of Ghost in the Shell or Ergo Proxy. The story paces slowly as further details about the monster are given. It was possibly produced in the late '90s to early 2000s, a few years before I watched it.
The focus of the movie is a rather generic monster: it walks on all fours, is adept at swimming, has olive skin, and a large tail. Also, at some point, it is discovered that it's pregnant. 
One of the main characters is a salty old detective who limps around. I think he has a cane which he hastily abandons in a chase scene (see next bullet).
There is a climactic point in which the detective is limping through a multilevel construction site whilst being pursued by the monster. There are large exosuits visible in the background (possibly used for construction).
In this same scene, the construction site undergoes some sort of emergency shutdown, during which the monster's large tail is cut off by a closing door. 
I'm not certain but I believe the monster dies in the end.


I'm sorry I don't remember any more details.
It is an arc in the Patlabor manga storyline. Most likely, you are talking about the Patlabor The Movie 3 (2002). It has also been adapted in the original late '80s OVA.