This Cracked article claims that Japanese soldiers in WWII would eat prisoners of war.

The article claims that there were a number of documented cases of Japanese soldiers engaging in cannibalism:

The document helped Tanaka uncover over 100 hushed-up cases of confirmed cannibalism by the Japanese Imperial Army, with them eating Australian and Indian soldiers, and even Asian citizens.

It further claims that these cases were known by higher command and sometimes even supported:

On many of these picnics, the soldiers weren't even starving. Instead, cannibalism was practiced under the supervision of the commanding officer as a team-building exercise, meant to strengthen the warrior spirit and consolidate interpersonal bonds

Is there evidence to prove these claims?

The above link is for a comedy website, but one that claims to provide accurate information in a comedic fashion. As the article claims to be reporting on true information, and it is known to have a large base of viewers, I believe this would qualify as a notable claim.

I'd like to note that this answer contains mentions of particular instances of cannibalism, and while no unnecessary details have been included, it may still be upsetting to some people.

Yes, undoubtedly so.

Stories of cannibalism by Japanese troops has been presented by both Japanese soldiers and prisoners they captured.

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  Various members of the Indian Army. Jemadar Abdul Latif was an early accuser.

  
  
  

  
  

  One of the first to level charges of cannibalism against the Japanese was Jemadar Abdul Latif of 4/9 Jat Regiment of the Indian Army, a VCO who was rescued by the Australians at Sepik Bay in 1945. He alleged that not just Indian POWs but even locals in New Guinea were killed and eaten by the Japanese.

  
  

  
  
  

  The same Times of India article lists several other prisoners of war as testifying that the same thing occurred at other camps. For instance, Captain R U Pirzai and Subedar Dr. Gurcharan Singh, Indian Army said

  
  
  

  
  

  Of 300 men who went to Wewak with me, only 50 got out. Nineteen were eaten.

  
  

  
  


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  Testimony at war crimes trials in the 1940s, unearthed by the historian (Toshiyuki Tanaka) mentioned in the Cracked article:

  
  
  

  
  

  Another archive contained testimony by Australian troops to war-crimes tribunals.

  
  
  

  An Australian army corporal recounted how he found the mutilated bodies of his comrades. One had only the hands and feet untouched.

  
  
  

  An Australian lieutenant described finding the dismembered remains of several bodies, saying: "In all cases, the condition of the remains were such that there can be no doubt that the bodies had been dismembered and portions of flesh cooked."

  
  

  
  


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  Documents from the United States military, as discussed in Researching Japanese War Crimes: Introductory Essays, contain many references to and reports of cannibalism:

  
  
  

  
  

  Records Regarding Pacific Area War Crimes Cases, 1944–49 has reports on the massacre of ninety-eight civilian employees of Pan American Airways on Wake Island accused of maintaining secret radio communication with U.S. naval forces following the island’s occupation by Japanese forces, as well as a number of cases involving torture and murder (including beheading and cannibalism) of downed U.S. flyers, and the executions of Catholic priests and other civilians suspected of spying or engaging in other anti-Japanese activity.

  
  

  
  
  

  and

  
  
  

  
  

  For example, Legal Section, Administrative Division, Area Case Files, 1945–48 has hundreds of case files, organized by location, that contain death certificates, affidavits, investigation and interrogation reports, and photographs. These documents pertain to various war crimes committed against Allied military personnel and civilians in Japan and elsewhere. The war crimes mentioned include cannibalism, beheadings of downed airmen, bayoneting of wounded soldiers, massacres of villagers suspected of spying, intentional bombardment of field hospitals, and torture of captured seamen aboard Japanese vessels.

  
  

  
  


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  Japanese soldiers themselves, in a number of cases, confessed to cannibalism. The same Associated Press article notes

  
  
  

  
  

  In Canberra, Australian National University war historian Hank Nelson said cannibalism took place in isolated fighting zones such as the Kokoda Trail, Sepik River and Bougainville Island.

  
  
  

  Nelson had also uncovered evidence of cannibalism. One young Japanese soldier confessed at a war-crimes trial he ate the flesh of an Australian he had shot in battle.

  
  
  

  "He simply said he did it out of intense hatred and intense hunger," Nelson said.

  
  

  
  
  

  That said, Tanaka himself says that cannibalism was often carried out by well-fed troops; in other words, it was not always a crime of desperation.

  
  
  

  A Time article from 1946 (I don't have access to the full article) begins by talking about the testimony of a major in the Japanese army:

  
  
  

  
  

  A U.S. military commission on Guam last week read into the record a Japanese Army major's confession of cannibalism. Unlike rumored instances elsewhere, this was no story of starving Japanese eating their own or enemy dead in an effort to survive. It was ritual cannibalism practiced on the bodies of U.S. flyers who had been decapitated after being shot down in the Bonin Islands. The sole excuse: "war madness."

  
  

  
  
  

  A member of the Japanese medical staff in a camp gave details to another historian:

  
  
  

  
  

  A Japanese medical orderly who helped the surgeon prepare the ingredients said: "Dr Teraki cut open the chest and took out the liver. I removed a piece of flesh from the flyer's thigh, weighing about six pounds and measuring four inches wide, about a foot long."

  
  

  
  
  

  This particular anecdote comes from the book Flyboys, a nonfiction book by James Bradley. It appears to describe the Chichijima incident. Several Japanese officers were prosecuted for their actions, and as there was no international law punishing cannibalism, they were only indirectly charged on that count:

  
  
  

  
  

  Lieutenant General Joshio Tachibana, Imperial Japanese Army, and 11 other Japanese military personnel were tried for the beheadings of two American airmen in August, 1944, on Chichi Jima in the Bonin Islands. They were beheaded on Tachibana's orders. One of the executed airmen, a U. S. Navy radioman third class, was dissected and his "flesh and viscera" eaten by Japanese military personnel. The U. S. also tried Vice Admiral Mori and a Major Matoba for murder in the deaths of five U. S. airmen, in February, 1945. Major Matoba confessed to cannibalism. However, military and international law had no provisions for punishment for cannibalism per se. They were accused of murder and "prevention of honorable burial."

  
  

  
  
  

  More information can be found in a United States military document:

  
  
  

  
  

  A charge entitled Neglect of Duty in Violation of the Laws and Customs of War was brought against Lt.-General Yoshio Tachibana and Major Sueo Matoba of the Imperial Japanese Army and against Vice-Admiral Kunizo Mori, Captain Shizuo Yoshii and Lt. Jisuro Sujeyoshi of the Imperial Japanese Navy, in their trial by a United States Military Commission at Guam, Marianas Islands, in August, 1946. The Specifications appearing under this charge alleged that various of the above accused unlawfully disregarded, neglected and failed to discharge their duty, as Commanding General and other respective ranks, to control members of their commands and others under their control, or properly to protect prisoners of war, in that they permitted the unlawful killing of prisoners of war, or permitted persons under their control unlawfully to prevent the honourable burial of prisoners of war by mutilating their bodies or causing them to be mutilated or by eating flesh from their bodies. The Prosecution claimed that there had been an intentional omission to discharge a legal duty. All of the accused mentioned above were found guilty of the charge alleging neglect of duty, and although a sentence of life imprisonment was the highest penalty imposed by the Commission on an accused sentenced on this charge alone, the trial does serve as further proof that neglect on the part of a higher officer of a duty to restrain troops and other persons under his control can render the officer himself guilty of a war crime when his omission has lead to the commission of such a crime.

  
  

  
  

The information comes from both sides, and as it seems that there is no particular reason for large numbers of Japanese troops to independently admit to a war crime if it never happened - given that many officers were being tried for said war crimes - the stories seem trustworthy.

Unfortunately, I have been unable to find definitive evidence that isn't oral testimony. Photographs, for example, would lend even more credulity to the claims; it's possible that some exist in classified documents. Still, the testimony that exists is quite convincing.