Heres a few points to considor about Japan.

1. Japan is highly mountainous, very vertical.

2. Theres is relatively little flat land.

3. Japan has a high population.

4. Japan is streached out over a long area, so most flat land is a little strip
between the sea and the mountainous interior.

Considoring these points, I'm not suprised Urban living seems awfully cramped.
They cant afford Gardens because land is always in high demand and short supply, in western Europe we have massive huge flood-plains and rolling terrain to build over to our hearts content, but relatively low population density, so we dont want or need to build over everything.
Saying that, from what i have gathered, the Japanese really do like to get out into the country.

Concrete works along rivers and hills near to cities are there to protect the cities, Japan needs to protect what flat land it has.
This does however seem to create a more noticable apathy towards nature in an urban setting, but its merely because the situation means a green urban enviroment for most Japanese isnt practical.

In my home city of Aberdeen we have plenty of gardens and tree's and green spaces but thats because were one small city with plenty of room for everyone who wants to live here.

The fact people spend good money to buy potted plants and stuff for outside the front of their houses is indication enough nature is important to them.
The only difference really is that:

1. The western world morally masturbates to nature to make ourselves feel like good noble people.

and:

2. The constraints of the crowded urban lifestyles of many Japanese means coupled with the demands on their time and energy means they just dont have days at a time to watch a bird sitting on a branch or watching a tree grow or whatever.

I love greenery and nature myself but yeah, I can see why many Japanese just dont have the time and space to get into it as deeply as westerners.

Maciamo: If your going to use secondary sources I would advice seeking out academic literature instead of more pop-lit type of stuff.
The book you linked too isnt a scientific study into the destruction of the enviroment of rural Japan, its a book about the opinion of one writer, in essence, its not much more valid and impartial then a republican rant about the evils of a democrat run America or something.

As entitled to their biased opinions as any given foreign visitor to Japan is, this doesnt make it fact.

I was in Japan just 3 months and even I saw enough of the country to know the claim that all but one rivers of japan are concreted up was false.
And I've never seen a concreted up mountainside ever, and I went on a drive through them to go fishing once.

I dont exactly know your first hand experiences of Japan, but if you never got out of mega-Tokyo, your not really in a position to make wild claims on all Japan, while if you have travelled around a bit, it would be suprising if you could sincerely claim to have seen every hillside and river concreted up.

I will agree though for various reasons gardens and nature being on the minds of most urban Japanese is rarer then Europe.

At the time he wrote the book, there was only one river in Japan that didn't have concrete anywhere from the beginning to the end (in Shikoku, if I remember well).
Thats unfair and you know it, very few rivers that run through a European city do so without concreted banks in places.

Concreted waterways arent the preserve of japan, where do you think they got the idea?, concreting a river bank in certain areas are there to ensure the banks remain stable for the nearby buildings, and to help control any rise in water flow, to help dampen or stop the effects of what would otherwise cause flooding.

Again, Japan is a country which in many places only has a thin strip of flat land between mountain and sea, where the effect of flash or severe floods can be even worse, and when flat-land is in such high demand, building right up to a river bank is sometimes the only option, and as such that bank needs to be stabalised and protected against flooding.