MANILA, Philippines (AP) _ A government auditor charged Thursday that deposed President Ferdinand E. Marcos channeled interest from a U.S. foreign aid fund into a secret account and used the money for unknown purposes.

The Philippine council that administered the U.S. Economic Support Fund, part of the U.S. compensation for American use of military bases in the Philippines, opened a ''confidential account'' of $6.25 million with interest from the fund, said auditor Edward Sanchez.

Marcos' wife, Imelda, headed the council, which worked jointly with the U.S. Agency for International Development in overseeing the fund.

The executive director of the council, J. Roberto Abling, withdrew an equivalent of $1.75 million from the confidential account in late January with vouchers that read ''as per instruction of the president,'' the auditor said.

Abling, who could not be reached for comment, deposited back $650,000 on Feb. 12, 14, and 15, but has not reported the whereabouts of the remaining $1.1 million, Sanchez said.

''The withdrawal represents just one of the hundreds of ways the Marcoses handled public funds illegally and unethically,'' Sanchez said. ''We expect to reveal other instances but we haven't yet compiled the documentation.''

The United States has given since 1980 some $459.6 million to the fund, aimed primarily at building schools, roads, and other public works for Filipinos living near U.S. military bases.

AID plans to disburse in 1986 a total of $179.6 million in economic aid to the Philippines.

An agency official, who spoke on the condition he not be identified, said the U.S. General Accounting Office did not find irregularities in how the Marcos government spent American aid, but acknowledged Philippine records uncovered since Marcos fled the country Feb. 26 could reveal wrongdoing.

Sanchez said the covert account was opened at the Land Bank of the Philippines based on interest from total U.S. payments to the fund deposited at the Philippine National Bank.

Sanchez said the covert account violated laws specifying projects to be funded by the interest the aid money earned. He said the alleged withdrawals by Abling would have violated laws that require that the purpose of the money be specified and approved by the chief accountant of the council.

Sanchez is a member of the government's Committee on Audit.

Last week, chief government auditor Teofisto Guingona disclosed that Manila Airport Manager Luis Tabuena withdrew an equivalent of $2.7 million from airport revenues in January, saying he intended to pay a construction company.

Guingona said Tabuena acknowleged that he withdrew the cash but said he gave it to the presidential secretary under orders from Marcos.