Women and Children in Conflict Protection Act of 2003

Women and Children in Conflict Protection Act of 2003 - Directs the Secretary of State to: (1) develop a strategy for the protection of women and children who are affected by a complex humanitarian emergency (a situation occurring outside the United States and caused by armed conflict, natural disaster, food shortage, or state-sponsored harassment or persecution, which results in a significant number of refugees, internally displaced persons, or other civilians requiring urgent basic humanitarian assistance) (emergency); and (2) designate coordinators to implement such strategy.

Requires such coordinators to: (1) maintain and disseminate a database of information on gender-based violence or exploitation of children during an emergency; (2) assist embassies and consular posts in responding to such risks; and (3) establish a gender-based violence or exploitation reporting and monitoring system for U.S. diplomatic missions and consular posts.

Prohibits any State Department refugee or migration assistance from being provided to an organization that has failed to adopt a code of conduct regarding the protection of beneficiaries of humanitarian assistance that incorporates six core principles (established herein) against sexual exploitation and abuse as recommended by the Inter-Agency Standing Committee. Requests all national, multilateral, and nongovernmental agencies to review and revise their administrative, management, and employment practices in refugee and displaced persons camps.

Requires each coordinator to: (1) ensure that U.S.-funded organizations that respond to an emergency have the necessary resources to address the specific health needs of women affected by the emergency; and (2) identify an organization or individual to facilitate the coordination and implementation of such activities.

Directs the Secretary to urge the United Nations High Commissioner for Refugees to work with nongovernmental organizations to design and implement a model whistleblower system under which humanitarian workers, refugees, and internally displaced persons can report instances of gender-based violence or exploitation of children.

Requires: (1) the State Department to work with certain entities to ensure that, in situations of long-term displacement, refugees and internally displaced persons are granted work permits and other documentation to enable them to generate legitimate income; and (2) a report from the Secretary on the development of protection initiatives for the prevention of gender-based violence and exploitation of children.

Directs the Secretary to: (1) develop and implement programs to assist communities that have been affected by an emergency and former combatants (women or children affiliated with an armed group); and (2) report on all current programs to assist nations to reconstitute civilian police authority and capability following an emergency.

Amends the Foreign Assistance Act of 1961 to authorize the President to provide assistance to promote the security of, provide equal access to basic services for, and safeguard the human rights and dignity of civilian women and children who are refugees, displaced persons, or inhabitants of areas affected by an emergency.