O'Brien was recently ousted as host of NBC's "The Tonight Show."
TVGuide.com said his decision not to play master of ceremonies for Broadway's biggest night may be due to his NBC exit contract, which "restricts him from certain activities until Sept. 1."
O'Brien is allowed to appear on television as of May 1 but is forbidden to speak negatively about the network, Playbill.com said.
The comedian is also scheduled to begin his live U.S. stage show "Legally Prohibited From Being Funny on Television Tour" April 12.
The tour is to run through June 14 and would conflict with the 64th annual Tony Awards presentation, which is to be broadcast live from Manhattan's Radio City Music Hall June 13 on CBS, Playbill.com noted.