Rai has been booked for alleged irregularities in awarding contracts for civil and electrical works for the Convention Centre to a private firm, CBI sources said.
The agency had sought the sanction of the Home Ministry to file a case against Rai who is considered close to Chief Minister Sheila Dikshit, the sources said.
The agency after getting the sanction has registered a case against Rai and is likely to carry out searches at the premises of suspects, they said.
The sources also said there was enough evidence against Rai and other NDMC officials in the alleged graft charges in the award of contract for construction and other activities at the New Delhi Convention Centre.
Rai, who is posted as Secretary Health and Family Welfare in Goa, was the chairman of the New Delhi Municipal Council between 2007 and 2011.
Dikshit in her letter to Chidambaram had defended Rai noting that a number of officers had to take certain decisions bypassing laid down norms and procedures to ensure speedy implementation of the CWG projects and due care must be taken in allowing any investigation against them.
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CBI sources said the Convention Centre was not a project under the Commonwealth Games.
The Delhi government had rejected the findings of the Shunglu Committee and CAG on the same grounds. Both CAG and Shunglu committee had slammed Delhi government for alleged irregularities in a number of CWG projects.