The Lokayukta had, in its report, had recently made the recommendation.
"On the basis of the report of the CFSL Chandigarh, the Haryana CM gave the order," an official spokesman said here.
The Chief Minister has also directed that the matter be referred to the State Vigilance Bureau.
He also directed that the suggestions made by the Lokayukta be implemented and a senior competent police officer deputed to investigate the entire case expeditiously on all counts of allegations of corruption levelled in the CD.
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Haryana Lokayukta Justice Pritam Pal (retd) had recommended registration of a case against Fauji.
Congress leaders had maintained that the allegations that they sought money in lieu of CLU permissions were baseless and the complaint was not maintainable by the Lokayukta under Section 9 of the Haryana Lokayukta Act.