Farm Risk Management Act of 2006 - Amends the Internal Revenue Code to: (1) establish tax-exempt farm risk management accounts to allow taxpayers engaged in the business of farming or ranching to use distributions from such accounts to offset operational losses in lieu of receiving, after a specified transitional period, federal subsidies to purchase crop insurance; (2) allow a tax deduction for cash contributions to such accounts; (3) specify minimum levels of contributions to, and maximum levels of distributions from, such accounts; (4) require the Secretary of Agriculture to make matching contributions to such accounts; and (5) set forth tax rules relating to account distributions, excess contributions, and prohibited transactions.