The ministry announced the probe on Sunday, a day after Modern Sport Club confirmed Refaat's death.
Refaat, 31, had previously suffered a cardiac arrest during a league match in March and spent weeks hospitalized.
Minister of Youth and Sports Ashraf Sobhy has assigned the ministry's legal committee to examine all documentation related to Refaat's travel outside the country, according to a ministry statement.
The committee will specifically investigate potential irregularities highlighted in recent media reports.
"The minister has also formed a committee of experts to conduct a further review of all documents related to Modern Sport Club, the Egyptian Football Association, and the Egyptian Olympic Committee," the statement added.
The ministry emphasized transparency and vowed to disclose all details and findings upon completing investigations.
Refaat's death comes as a blow to Egyptian football. He debuted with Egypt’s senior national football team in 2013 and made seven appearances with the Pharaohs.
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