The HC directed that fresh elections be conducted within a period of five months.
A bench of justices S Ravindra Bhat and Najmi Waziri also appointed former chief election commissioner S Y Quraishi as an administrator to look into the functioning of the AIFF.
"AIFF is not aware of the reasons of the Hon'ble Delhi High Court to pass this order. Once AIFF receives the copy of the Order from the Hon'ble High Court, AIFF will decide the course of action in accordance with the law," a statement from the AIFF said.
The AIFF said that the HC in its order dated December 15 last year had observed that the election ought to be conducted as per the applicable rules of the institution concerned and also in consonance with the National Sports Code and the elections guidelines contained with respect to conduct and eligibility conditions including age, tenure and restrictions.
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"AIFF also apprised the Hon'ble High Court that the Constitution of AIFF is in compliance with the terms of age limit, tenure limit of prime office bearers and one state-one vote policy. Accordingly, the Hon'ble Court allowed AIFF to proceed with elections vide its order 20th December 2016," it said.
"AIFF is fully compliant with all statutory regulations in terms of the Registrar of Societies Act as well as other notifications and orders of the Ministry of Youth Affairs and Sports. The Ministry of Youth Affairs and Sports also confirmed and verified in the past that that AIFF's election was in strict compliances with its Constitution and National Sports Code," the AIFF said.
"AIFF's election process is as per the FIFA and AFC statutes as well."
Patel, a former Union Minister, served as acting president of the AIFF for one year after long-time head Priya Ranjan Dasmunshi suffered a cardiac arrest in 2008. He took over as full time president in October 2009 before being re- elected for the top job in December 2012.