The Securities and Exchange Commission yesterday accused the Charter Co. of improper accounting practices in the 1981-83 sale of single-premium deferred annuities by its insurance subsidiaries. The Jacksonville, Fla., oil refining and marketing company settled the complaint without admitting or denying the commission's finding.

The parent company declared Chapter 11 bankruptcy last year, although the subsidiaries did not. Nevertheless, nervous policyholders, mindful of the troubles of another annuity purveyor, Baldwin-United, began selling off their policies at a rapid rate. Charter has since agreed to sell its insurance subsidiaries.

The SEC's action is significant because it sets out for the first time the accounting treatment required for the once-popular single-premium deferred annuities. The commission held that they should be considered investment contracts and that the income they generate should be spread over the life of the contract rather than counted up front.

According to SEC documents, Charter counted 35 percent of the income up front. As a result, its earnings for the years in question were materially greater.

Moreover, the SEC said Charter neglected to disclose in its annual report for 1981 the effect of considering as "rollovers" contracts that were actually terminated and reissued so that customers could get the benefit of higher interest rates.