UN spokesman Stephane Dujarric on Friday said Secretary-General Kofi Annan turned down the request because Baghdad has the death penalty.
Dujarric said the request was rejected in part because "serious doubts exist regarding the capability of the Iraqi special tribunal to meet relevant international standards".
"The secretary-general recently stated that UN officials should not be directly involved in lending assistance to any court or tribunal that is empowered to impose the death penalty," he said.
Another reason prompting the rejection was that the UN had no mandate to help train Iraqi judges.
Annan's rejection follows a week-long training session in London for Iraqi judges and prosecutors chosen to try Saddam and his key associates.
The London courses were organised by American lawyers. After they ended on Monday, both Iraqis and their Western advisers agreed that Iraqis were unprepared to undertake fully fledged trials soon.
The UN is, however, assisting in Iraqi elections planned for January by training Iraqi elections workers in Mexico and other places outside the country.
Dujarric said 6000 Iraqis had completed direct or indirect training and were setting up 585 voter registration stations.