"The consent to have investigation into the alleged misappropriation and diversion of funds for the scheme has been given by the concerned minister (of Ministry of Rural Development," Additional Solicitor General Indira Jaising told a bench headed by Chief Justice S H Kapadia.
The ASG said since the Centre has taken a decision to entrust the investigation, a notification in this regard will be issued.
Advocate Prashant Bhushan, appearing for the NGO, Centre for Environment and Food Security, which has filed a petition on the issue, said the court can direct the CBI to register an FIR.
However, the Bench asked the Centre to issue notification for the CBI probe within two weeks.
The government decided to order CBI probe as the apex court during the last hearing on March 14 had clearly said that if the centre failed to take decision within four weeks, it would step in to pass an order for CBI investigation.
Jaising placed before the bench a letter written by the Ministry of Rural Development to the CBI last week to probe the "alleged corruption and irregularities in the implementation of MNREGA (Mahatma Gandhi National Rural Employment Guarantee Act)".
In the April 4 letter addressed to the CBI Director, the Department of Rural Development, said "it has been decided to refer the Orissa case to the CBI".
"You are requested to kindly have the matter investigated and cause to initiate criminal proceedings against the delinquent officials under the relevant laws," the letter to the CBI said asking its Director to take the case on priority.
The Court also directed the Orissa Government to file an affidavit stating as to what extent the directions of the Centre has been implemented relating to the scheme.
During the last hearing, the bench had asked the Orissa Government to tell the reasons why it has not implemented the guidelines issues by the Centre for MNREGA.
Meanwhile, over the allegation of diversion of funds in Uttar Pradesh and Madhya Pradesh, the bench said it would take up the issue in the next hearing.
The apex court was hearing a public interest litigation filed in 2007 by the Centre for Environment and Food Security, alleging large-scale corruption in the implementation of the programme for rural job under the scheme which provides for legally-guaranteed 100 days of employment to at least one member of each rural household.