"I handed in those cheques (from Taiwan) for their appropriate use at all times," said Flores yesterday, who was president from 1999-2004.
President Mauricio Funes last month suggested to reporters that the missing funds might have been skimmed or misused, and said prosecutors would call Flores in for questioning.
Funes recently charged that three cheques -- for USD 1 million, USD 4 million and USD 5 million -- were issued by the Bank of New York, on behalf of Taiwan, and endorsed by Francisco Flores.
Funes said Taiwan donated the money to El Salvador in the waning months of Flores' presidency, between 2003 and 2004.
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But Flores firmly rejected the president's charges about his depositing the funds in his private accounts.
"I would like to say that I have never deposited a check from Taiwan's government in any account; that is key for me, to make clear that I have never deposited a check from Taiwan's government in any account," he stressed.