Federal Deposit Insurance Modernization Act of 1986 - Amends the Federal Deposit Insurance Act to apply the Federal Deposit Insurance Corporation's annual investment income to its annual operating and insurance costs before determining its net assessment income. Requires the amount of costs exceeding income for a calendar year to be deducted, first, from the Corporation's investment income for the subsequent year and then from total assessments for such subsequent year. Requires any excess investment income for a calendar year to be transferred to the Corporation's capital account. Requires the Corporation's Board of Directors to maintain the ratio of the Corporation's capital account net of assets held in the form of Federal Deposit Insurance capital notes to the Corporation's total capital account at not less than 25 percent. Authorizes Corporation-insured banks to issue Federal Deposit Insurance capital notes. Directs the Corporation, as of December 31 of each calendar year, to invest the amount of its net investment income transferred to its capital account in such notes pro rata among such banks based on each bank's assessments for such year. Requires each bank to invest the amount obtained from such notes in obligations of, or insured by, the United States, except that a bank may use part of such amount, temporarily, in order to satisfy temporary liquidity needs. Deems notes held by the Corporation to be primary capital of the issuing banks. Directs the Comptroller General to conduct and report to the Congress on a semiannual audit of the note program.