Care, which was the only UK-based charity operating in central and southern Iraq before the war, is concerned about the influx of inexperienced relief agencies since the end of the conflict.
"There is a real danger of parallel systems developing," said a spokeswoman for Care. "Iraq might have been a failed state in some ways, but not in terms of the administration of things like health, education and refuse collection.
"It's important to resurrect systems that were there before. NGOs need to co-ordinate with each other and back up indigenous systems, not reproduce them."
In previous post-conflict situations such as Kosovo and Afghanistan, the intervention of large numbers of relief agencies caused serious logistical problems and disrupted the work of agencies already operating there.
Margaret Hassan, director of Care Iraq, said charities should not open separate health clinics that undermine the Iraqi health service. "We need to help that health service get back on its feet and provide a proper service, a better service, but not to run a parallel service."
Paul Anticoni, head of international aid at the British Red Cross, agreed that aid agencies were in a difficult position. He said: "There is a vacuum at the moment and a need to provide emergency repair work for services.
The risk is that you take the role of a de facto administration. We wouldn't want to be part of any process to establish new governance for Iraq.
"International humanitarian organisations shouldn't replace or substitute national services."
Care, along with Save the Children and Christian Aid, is to tell MPs about the difficulties of delivering supplies to Iraq. The charities will make submissions to the Parliamentary Committee on International Development ahead of the select committee's questioning of new international development secretary Baroness Amos on her department's role during the conflict.
Meanwhile, the Disasters Emergency Committee has said no decision had been made on whether to launch an emergency appeal on behalf of UK aid agencies in Iraq.
Brendan Gormley, chief executive of the committee, said the situation was being reviewed "on a weekly basis" and an appeal could be triggered if the humanitarian situation worsened.