CBI sources said the complaint received from the Delhi government which has been converted into an FIR by it also mentions alleged role of Chief Minister Arvind Kejriwal and Deputy Chief Minister Manish Sisodia.
However, the CBI FIR has been registered against Khan and unknown persons under IPC sections related to criminal conspiracy and provisions of Prevention of Corruption Act related to criminal misconduct and corruption.
It alleged that another Waqf Board was constituted and its Chairman was elected under the directions of Deput Chief Minister of Delhi in contravention of Waqf Act, 1955 and Delhi Waqf rules of 1977, the sources said.
The CEO of new Waqf Board and over 30 staff members were appointed and employed by the Waqf Board in contravention of section 24 of the Waqf Act, 1955 and Delhi Waqf Rules, 1977, they further said.
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The CBI FIR alleged that irregular and illegal appointment of officials led to the loss of revenue of Delhi Waqf Board and appointments were done by misusing the official position as public servants.
It is alleged that Waqf Board properties were leased to the tenants and the encroachers were allowed to possess the properties in contravention of lease rules, 2014 leading to the loss of revenue/assets for the board.
It was done by misusing the official position by the public servants, it alleged.
"We do not comment on the basis of hearsay," Delhi government spokesperson said when asked about comments on the development.
Khan had maintained that recruitments at the Board were conducted with due legal process and had alleged that Jung was creating "hindrance" in working of the body.
"In view of the deliberate and persistent acts of illegality, violation of rules, allegations of corruption, possibility of mala fide etc, the whole matter related to Delhi Waqf Board is referred to the CBI for investigation," the L-G office had said in a statement.
Kejriwal government had superseded the erstwhile Board was in October last year and all its powers and duties were transferred to the secretary (revenue).
Khan was unanimously elected as the new chairman of the reconstituted Board by its members in March.
The Board faced charges of corruption in appointments made under the tenure of Khan and the ACB launched a probe into the alleged "recruitment scam" on a complaint of one Mohammad Mustafa in September.
The Anti-Corruption Branch had raided Waqf Board office on September 8 and questioned Khan.