Fairchild Industries owes the federal government $39 million in back taxes and penalties for the years 1965 through 1972 because of allegedly fraudulent tax returns, according to the Internal Revenue Service.

In IRS documents filed in the U.S. Tax Court here, the agency disclosed that it is questioning accounting practices and deductions by the Montgomery County areospace and communications company.

Among deductions being challenged is a cash fund allegedly used for "political contributions and other non deductible payments."

The first hint of a possible IRS claim against Fairchild was published in the firm's recent annual report for 1977. Fairchild said at the time that the IRS intelligence and audit divisions were studying tax returns from 1965 through 1975 and that the government investigators were interested primarily in costs associated with foreign sales and other expense items.

Although Fairchild did not disclose earlier the extent of IRS claims, informed sources speculated that the total was about $40 million.

In the Tax Court documents, the IRS said it is seeking $24.6 million in alleged tax deficiencies and another $14.4 million in penalties because "all or part of the underpayment . . . is due to fraud."

Fairchild denied that it owes either the back taxes or penalties abd restated an annual report assessment that "no fraudulent tax returns have been filed and that the amounts provided for income tax liabilities are adequate."

Fairchild Chairman Edward Uhl has stated that his firm did not join aerospace competitors in making questionable overseas payments to win business and the firm said two years ago that an internal study found no material payments between 1970 and 1975.