Simon Ebhojiaye, Director of Federations and Elite Athletes Department (FEAD) in the ministry, disclosed this in a statement on Friday.
He said the minister had stepped in to stem and address all issues causing disaffection among Team Nigeria athletes at the Games.
The News Agency of Nigeria (NAN) reports that 10 Nigerian athletes had been disqualified due to administrative lapses regarding meeting three pre-Olympics anti-doping tests.
The captain of Team Nigeria, Aruna Quadri, has also complained over poor welfare, while Blessing Okagbare has spoken out against mismanagement of athletes’ affairs.
Ebhojiaye however explained that payment of allowances to athletes commenced last week and was still ongoing.
He said the minister had on Thursday in a meeting apologised directly to the 10 track and field athletes disqualified and assured them of their welfare.
“The minister also pledged to fully investigate circumstances leading to the unfortunate development with a view to halting any reoccurrence.”
The director also said issues relating to the International Olympic Committee (IOC) packs/phones for the athletes was also resolved by Dare.
He added that no official of Team Nigeria or the Nigeria Olympic Committee (NOC) took away any entitlements of any athlete.
“No official of Team Nigeria or NOC took away entitlements of any athlete as being wrongly reported.
“Therefore, issues over the phone were resolved administratively and according to the IOC Rules and Guidelines.
“Team Nigeria officials acted in line with IOC standards and as soon as approval was received the right thing was done,” the ministry official said.
NAN reports that the IOC had approved that the 10 Nigerian athletes, who were disqualified due to no fault of theirs, should also receive the Samsung Galaxy S21 5G phone.
The phones were distributed to athletes at the Games Village.
The letter of approval for the phones’ release was signed by Jonas Brun, Junior Project Manager, IOC Relations/IOC Services.
“Regarding your athletes that will not participate in competitions in Tokyo in light of the latest information received, I confirm that you can still go ahead and give phones to the athletes,” the letter read in part.
The phones were meant for athletes to benefit from all important information included in the Athlete365 website and also to comply with requirements set forth in the Olympic playbooks.
These were in particular the download and use of the apps required by the Japanese authorities.
Some of the disqualified athletes, due to the alleged negligence of Nigerian officials in not ensuring that they undertook the three out-of-competition tests in the build-up to the Olympics, staged a protest in Tokyo on Friday.
They accused the Athletics Federation of Nigeria (AFN), Federal Ministry of Youth and Sports Development and the NOC of negligence leading to their disqualification. (NAN)

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