Basically in Tang China they did not take the Vinaya overly seriously. Ordination certificates were bought and sold. Even in the more orthodox Buddhist community, the practice of the Vinaya was only partially implemented and observed. This was the same in Japan. The "Vinaya school" was seen as a school of thought and practice which need not be universal, just as, for example, Abhidharma is an optional field of study.
Consequently, in such circumstances the Japanese monk Saichō 最澄 (767–822) devised a new monastic system based on the bodhisattva precepts from the Brahma Net Sūtra
. He did not abandon the Vinaya, but saw it as merely provisional and such ordinations were to be carried out only after having a very solid foundation in Mahāyāna. There are doctrinal reasons for this. The Lotus Sūtra
suggests the bodhisattva have little to do with the Hīnayāna. It logically follows you avoid the Vinaya, too.
I wrote all about this here if you're interested:https://sites.google.com/site/dharmadep ... os-reforms
Also, bear in mind Buddhism in China often functioned without much of a full Vinaya at all. Again, shameless self promotion:http://huayanzang.blogspot.com/2013/06/ ... inaya.html
I believe it was around the Kamakura period that Vinaya ordinations more or less faded out of existence. I believe one big reason for this was the power of Tendai, which despite Saichō having said Vinaya ordinations were to be carried out as the last component to his new system, they dropped the Vinaya altogether. This was probably more to do with power politics than anything else. Legal Vinaya ordinations were not necessarily under the jurisdiction of the Tendai school, whereas the bodhisattva monk ordinations were.
The truth is though the Vinaya was largely irrelevant to the Japanese Buddhist community, as it was in China (however alternative models like the Conglin system in Chan were developed). Kūkai had insisted on the Vinaya, but Shingon likewise dropped the Vinaya as well. There's a good article on this:http://nirc.nanzan-u.ac.jp/nfile/2884
As for married clergy, it was in 1872 that the Meiji government government issues proclamation 133 on April 25th:
Hereafter monks may freely eat meat, marry and keep hair. Furthermore, there will be no penalty if they wear ordinary clothing when not engaged in religious activities.
Before this there were a lot of covert marriages, but this simply decriminalized such activities. Within three generations the vast majority of Japanese clergy were married with children despite what the sect authorities had to say.
Here's another good article:http://www.scribd.com/doc/175714110/Mei ... ge-Problem