Emergency Assistance for Depository Institutions Amendments of 1986 - Amends the Federal Deposit Insurance Act to permit the Federal Deposit Insurance Corporation (FDIC) to authorize the following actions with respect to an insured bank with total assets of $100,000,000 or more that is closed or in danger of closing: (1) the merger or consolidation of the bank with another institution; (2) the purchase of the bank's assets by another institution; or (3) the assumption of the bank's liabilities by another institution. Provides that such total asset requirement shall not apply to agricultural banks for three years after enactment of this Act. Eliminates provisions setting forth priorities for FDIC consideration in authorizing any such action and directs the FDIC to consider only: (1) the need to minimize the cost of financial assistance; and (2) the maintenance of specialized depository institutions. Amends the National Housing Act to permit the Federal Savings and Loan Insurance Corporation (FSLIC) to authorize the emergency acquisition of any insured institution which: (1) is in default or in danger of default; or (2) poses a risk to the FSLIC by reason of severe financial conditions affecting such institution. Eliminates provisions setting forth priorities for FSLIC consideration in authorizing such an acquisition and directs the FSLIC to consider only: (1) the need to minimize the cost of financial assistance; and (2) the maintenance of specialized depository institutions. Requires the FDIC and the FSLIC to exclude any unusual and infrequent transactions of an insured bank or institution in determining whether such bank or institution has incurred losses during two quarters for purposes of the net worth certificate program. Amends the Garn-St Germain Depository Institutions Act of 1982 to: (1) make permanent the emergency acquisition provisions of the Deposit Insurance Flexibility Act; and (2) extend the Net Worth Certificate Act for three years.