The IIIHF revealed that Japanese players and officials have lost friends and colleagues in the disaster.
"What we are witnessing in Japan is one of the biggest natural disasters in recent memory and the consequences of the earthquakes and tsunamis are catastrophic," said IIHF President René Fasel.
"As ice hockey in Japan is concentrated to the northern parts [of Japan], we know that many of the athletes selected to represent their country and also the officials have been directly or indirectly affected by the disaster.
"We recognise with full sympathy the need of the athletes and officials to be with their loved ones during the very difficult times of mourning and national recovery."
The IIHF said Japanese ice hockey's governing body had stated its moral obligation to forgo participation in three World Championship tournaments, including the event for second ranked teams in Budapest next month.
They have also withdrawn from the women's World Championhip Division One in Ravensburg, Germany, and the under-18 World Championships Division ONe in Riga, Latvia.
"Although we regret the absence of the Japanese athletes at our championships, this is a time where sporting activities become almost irrelevant," said Fasel.
"Our thoughts are with the Japanese people who have suffered immeasurably during the last weeks and we know that it will take many years to overcome the damages.
The IIHF sent a letter of condolences to the Japanese association.