"We are sorry to inform you that the Japanese team cannot participate in the Copa America 2011 in Argentina," the Japanese Football Association (JFA) said in a letter to the Argentine Football Federation. "We apologise deeply."
Japan and Mexico were invited as teams from outside South America to play in the regional tournament in July, where the Japanese had been drawn in Group A with the hosts, Bolivia and Colombia.
But their attendance was cast into doubt after the huge earthquake and tsunami laid waste to much of the country's Pacific coast.
Initially the JFA said it would send the national team in spite of the devastation, but it has struggled to convince European clubs to release their Japanese star players ahead of the start of the new season.
"Under the current circumstance, we cannot form a team competitive for Copa America," JFA President Junji Ogura told reporters in Tokyo.
"Based on the judgement, we have unfortunately decided to decline," Ogura said. "It is extremely regretable."
The twin disasters of March 11 severely damaged a nuclear power plant in Japan's northeast, causing widespread electricity cuts that forced the temporary suspension of the J-League.
J-League clubs had agreed to cooperate with Japan's participation in the Copa America on condition that Europe-based players made up the bulk of the national squad coached by former AC Milan boss Alberto Zaccheroni.
Many of Japan's top players moved to Europe after the Blue Samurai reached the last 16 in South Africa last June in their best ever World Cup finish on foreign soil.
Japan's squad is usually spearheaded by CSKA Moscow midfielder Keisuke Honda, Borussia Dortmund goal machine Shinji Kagawa and Stuttgart striker Shinji Okazaki.
Left back Yuto Nagatomo, now on loan to Inter Milan from Cesena, is a key defender for Japan, along with Uchida.