In 2006, he was one of two players from the Hiroshima Toyo Carp selected to play in the 2006 World Baseball Classic, along with Takahiro Arai. He was touted as one of the obscure but key players on the Japanese team along with, then current, MLB players Akinori Iwamura and Kosuke Fukudome, but was injured getting hit by a baseball off the bat to the right hand during a practice game on February 24, forcing him to withdraw from the competition.
Kuroda obtained free agency on May 31, 2006, and announced that he was willing to hear offers from other teams. The Hiroshima Toyo Carp had a staunch policy against free agency because it would lead to higher salaries which the team would not be able to provide due to lack of financial structure. The team's management traditionally never attempted to re-negotiate with players of their own team who declared free agency (for example, the team ignored outfielder Tomoaki Kanemoto's offers to reconsider staying on the team because he had already declared free agency). Numerous teams showed interest in Kuroda, including the Seibu Lions and Hanshin Tigers, who had lost their key starters Daisuke Matsuzaka and Kei Igawa to the posting system. The well-financed Fukuoka SoftBank Hawks aggressively pursued Kuroda, while the Chunichi Dragons and Yomiuri Giants, who had been in pursuit of free agent Michihiro Ogasawara, were also thought to have interest.
Despite the team's anti-free agent policy, the Carp was facing serious problems with its weak pitching staff, which had kept them in the bottom half of the standings since 1997. The prospect of losing Kuroda, by far the most effective and consistent pitcher on the team, forced them into negotiations. On October 15, 2006, the team offered a 4-year, 1 billion yen deal with post-retirement benefits, showing that they were absolutely intent on retaining Kuroda. In terms of base salary, Kuroda had been paid 200 million yen in 2006, and this contract would only give a 50 million yen increase for 2007, with no further increases over the next three years. However, this was a major step-up for the Carp management considering that only two other players on the team (Tomonori Maeda and Tomoaki Kanemoto) had ever been paid more than 200 million yen per year. On November 6, 2006, Kuroda agreed to a 4-year 1.2 billion yen deal (250 million yen base salary+bonuses) to remain in Hiroshima. This new contract included a provision that Kuroda would be able to negotiate with major league teams as a free agent at any point during the 4-year deal. At the same time, Kuroda announced that he would play for no other Japanese teams besides the Hiroshima Toyo Carp. Although the deal ultimately concluded with a salary increase, Kuroda's negotiations showed a rare instance where free agency did not inflate salaries to ridiculous amounts.