The AIFF executive committee, which met in New Delhi with president Kalyan Chaubey in the chair, also approved the appointment of Karnataka official Satyanarayan M as the acting secretary general.
"The (Executive) Committee ratified the decision to terminate the contract of Dr. Shaji Prabhakaran as the Secretary General, and appoint Mr. M Satyanarayan as the Acting Secretary General of the All India Football Federation," a release said.
The 51-year-old Prabhakaran was sacked on Tuesday from the post of secretary general with Chaubey serving the termination order two days before the executive committee meeting.
Satyanarayan, who was recently appointed as the deputy secretary general, said the AIFF executive committee was "unanimous" in ratifying the decision to terminate Prabhakaran.
"There was no objection from any member of the executive committee, it was a unanimous decision (to ratify the termination of Shaji Prabhakaran as Secretary General)," Satyanarayan told PTI.
Four members, including former India captains Bhaichung Bhutia and Climax Lawrence, were absent.
Prabhakaran's sacking came 14 months after his appointment to the post even as the national federation did not mention what the breach of trust was that prompted the action. He had described his termination as "conspiracy".
He had also challenged the constitutional validity of the termination decision, saying that it did not get prior approval from the Executive Committee of the AIFF. Vice president NA Haris had, however, said that the president can appoint and remove a secretary general since the post is a paid one.
During the meeting, Chaubey said that the National Football Championship for the Santosh Trophy, which will be held in Arunachal Pradesh this season, will be known as the FIFA Santosh Trophy.
"I am happy to announce that after having discussions with FIFA, the Santosh Trophy will now be known as the FIFA Santosh Trophy. This entails that a team of FIFA officials will come to have a meeting with Arunachal Pradesh officials on the conduct of the tournament," said Chaubey.
"We also expect the FIFA President (Mr Gianni Infantino) to be present for the final on March 9 or 10,” he added.
Asked what is the significance of naming the tournament as FIFA Santosh Trophy, Satyanarayan said, "Some FIFA officials will be involved in the organisation of the tournament.
"Since FIFA will be a part of the organisation, there will a certain standard we have to maintain during the tournament. So, it will benefit everybody."
He was, however, non-committal when asked if FIFA will also give some financial support to the AIFF in organising the Santosh Trophy.
Chaubey said that the AIFF officials will hold detailed discussions with FIFA’s Chief of Global Football Development and renowned coach Arsene Wenger, who is set to visit India from November 19-23 to chalk out plans for the proposed FIFA-AIFF academies.
"Our plan is not to have one, but five academies, one across each zone in India. India being a big country, I personally feel, one academy will not be enough, since it could throw up only 25-30 players in one batch. So, we have taken up this ambitious project of five academies.”
He also informed the members about plans to establish a goalkeepers’ academy to produce quality custodians. Himself a former India goalkeeper, Chaubey told the members that he had a meeting with legendary German goalkeeper Oliver Kahn, who was in India recently on a personal visit.
Chaubey’s suggestion that some of the I-League matches should be played in some cities of Jharkhand, Bihar and Uttar Pradesh in order to spread the game far and wide was accepted by the Executive Committee.
The Executive Committee condoled the death of former India players Mohamed Habib and Prabhakar Mishra, and observed a minute's silence to pay respect to them.