Are war criminals still war criminals if the trial was unsound?

The Japan Times reports that:

Masahiro Morioka, parliamentary secretary for health, labor and welfare, said Thursday that Class-A war criminals convicted by the Tokyo War Crimes trial after World War II are not criminals because the tribunal was "one-sided."

Japanese government leaders have said that Morioka's position does not represent the government, saying that Tokyo has accepted the results of the tribunal.

Morioka is on the right wing of the ruling LDP, which puts him very close to the unpleasant militaristic, racist elements in Japanese political life, and his comments should be understood as the insult to other Asian countries that they were probably intended as. (See the Japan Times report for the reaction of the Chinese authorities, who never sound so reasonable or representative as when right-wing Japanese politicians give them this kind of chance.)
Having said that, the trials were undoubtedly not as carefully conducted as they should have been, nor did they have a wide enough remit.

one of the judges [in the Tokyo war crimes trials], Radhabinod Pal of India, issued a blistering dissent, attacking the Tokyo trial as an instrument of U.S. political power and argued that neither war crimes or conspiracy had been proven.

Pal condemned the court's decision not to allow the defendants to bring evidence about the atomic bombings of Hiroshima and Nagasaki, and compared then president Harry Truman's use of nuclear weapons to Germany's atrocities in World War I and II.

"If any indiscriminate destruction of civilian life and property is still illegitimate in warfare, then, in the Pacific war, this decision to use the atom bomb is the only near approach to the directives of the German emperor during the first world war and of the Nazi leaders during the second world war," he wrote. "Nothing like this could be traced to the credit of the present accused."

(from a rather odd article on the Asia America site)

Japanese jingoists like Morioka tend to agree with Pal (for all the wrong reasons, no doubt). A criticism they would not make is equally important. Many people who may have committed war crimes were never brought to trial, from the emperor (a political decision by the US administration) to low-ranking soldiers, as documented for example by Michael Goodwin, in his excellent book 'Shobun: A Forgotten War Crime in the Pacific' about the shobun ('disposal') policy of summary execution for captured airmen -- "by beheading, gunshot and even poisoning."

So the trials of the leaders in Tokyo were largely show trials: carried out by the US authorities for their effect on Japanese and US public opinion. But that doesn't mean that those convicted were not guilty: most of them undoubtedly were. In particular those who were cabinet members during the war were obviously culpable.