The foundation led by the KMT elder has been mired in controversy for several months, with accusations intensifying and family members intervening.
Claims of financial irregularities at Ma's foundation have escalated into criminal charges, public exchanges of blame among longtime associates, and an unprecedented involvement by his relatives.
The conflict has also sparked broader concerns regarding Ma's health, his political legacy, and the potential impact on the main opposition party, the Kuomintang (KMT), as local elections approach later this year.
Ma's team accused the two individuals of major financial infractions, such as distributing employee bonuses in cash and failing to accurately record a donation from a Taiwanese businessman operating in mainland China.