Protection of Family Farmers and Family Fishermen Act of 2003 - Amends the Federal bankruptcy code to reenact Chapter 12, Adjustment of Debts of a Family Farmer with Regular Annual Income (thus reinstating permanently family farmer bankruptcy relief).

Cites circumstances under which the claim of a governmental unit that arises from the disposition of a farm asset used in the debtor's farming operation shall be treated as an unsecured claim not entitled to priority.

Increases from $1.5 million to $3.237 million the maximum aggregate debt that permits a farming operation to qualify as a family farming operation for debt adjustment purposes. Decreases from 80 percent to 50 percent the minimum percentage of aggregate, noncontingent liquidated debts arising out of such a farming operation.

Modifies the requirement that a family farmer and spouse receive over 50 percent of income from farming operations in the year before a bankruptcy petition is filed. Allows the family farmer to meet the over-50-percent requirement in either the preceding taxable year or each of the second and third preceding taxable years.

Prohibits: (1) retroactive assessment of disposable income; and (2) post-confirmation modification of a bankruptcy plan that would increase the amount of payments that were due before such modification. Requires debtor's consent for post-confirmation increase in payments.

Extends Chapter 12 coverage to family fishermen whose aggregate debts do not exceed $1.5 million, of which at least 80 percent of aggregate noncontingent, liquidated debts arise out of a commercial fishing operation.