Some Malaysian news report for additional information.
Local Malaysian media reported that Mr Anwar's visits in 2006, 2009 and 2012 were done with prior visa application. Since middle last year, Japan had allowed 30 days visa free travel, however, those with past prison sentence served need to still apply for visa.
In this report,
ツ'I never blamed Wisma Putra for Japan fiasco' | Free Malaysia Today, Mr Anwar said that his office had made prior checks with the Japanese Embassy in KL whether he needs visa, but the Japanese embassy denied there were any calls or letters from Mr Anwar's office on his current visit. The last paragraph of that article certainly show that the Japanese Embassy is pressing Mr Anwar's office whether any inquiries were actually made. In other reports, the Japanese Embassy also said that the Narita authorities had asked Anwar whether he would like to appeal but he did not do so
ツ'Anwar did not follow procedure' - Nation | The Star Online.
Mr Anwar's Justice Party's Youth Wing made a noisy protest (attendedit seems by about a dozen individuals) in front of the Japanese Embassy and burned poorly painted Japanese flags while calling for a boycott of Japanese goods, which later got a resounding scolding by Mr Anwar himself
Anwar berates PKR Youth for stomping on Japan flag | Malaysia | The Malay Mail Online.
The Malaysian blogosphere is also filled by at least four rather unlikely explanations of the so-called "hidden hands" and "secret reports" claims by Mr Anwar. First, that the Japanese govt was bribed by the Malaysian government to bar Anwar's entry. Second, that the Japanese govt is vying for high speed rail contracts in Malaysia so Japan is totally willing to do whatever the Malaysian govt is asking. Thirdly, that the Japanese govt is upset by claims by Mr Anwar's opposition coalition that Japan paid some US 70 billion in compensations for World War 2 attrocities in the 1990's and these were pocketed by the govt (in reality war claims were paid in the 1960's, the sum was much smaller, I think a few million dollars), Fourthly, the Japanese authorities barred Anwar's entry because he was invited by a Yakuza linked organization to give a talk on Islam and democracy.
Personally, I think somebody in Mr Anwar's staff did not do his or her job in clarifying his travel arrangements with the Japanese Embassy, if any clarification was actually asked. The whole matter seems to have been blown out of proportion once Anwar claimed there was some sort of conspiracy. The Japanese, as usual,were sticklers for formality and bureucracy, though at least the Narita authorities gave Anwar the chance to appeal but Anwar did not do so.