The Board of Control for Cricket in India (BCCI) missed a deadline to name a squad for the tournament after the International Cricket Council (ICC) changed its revenue-sharing model.
However, a BCCI statement said it "unanimously decided that the Indian cricket team will participate".
A meeting to select the team will now take place on Monday, 8 May.
The initial deadline to name a Champions Trophy squad was 25 April but India will not face a sanction for not doing so.
At a recent ICC meeting, the BCCI was outvoted 13-1 in a bid to halt the revised deal which considerably reduces India's share from global events in the 2015-2023 cycle.
Acting BCCI secretary Amitabh Choudhary will now continue to negotiate with the world governing body over the issue.
The BCCI statement added: "The board unanimously authorised the acting honorary secretary of the BCCI to continue negotiations with the ICC in the best interest of the BCCI, while keeping its legal options open."
India have confirmed they will compete in the Champions Trophy being held in England and Wales from 1-18 June.