Louis Michel, the EU's development commissioner, will discuss the practicalities of setting up the job centre during a trip to Bamako on February 8.
The EU has been struggling to contain illegal migration to Europe by Africans searching for jobs and a better life.
More than 31,000 sub-Saharan migrants reached Spain's Canary Islands alone last year, six times as many as in 2005.
Malta and Italy faced similar problems. Thousands of would-be migrants are believed to have died during the perilous journey.
"We want migrants to come here legally then go back to their countries of origin when their contracts have ended," Frattini said.
"People can have guaranteed periods of work and illegal undeclared labour will be combated in a very stringent way."
The centre will also aim to increase jobs in Africa by promoting investment in labour-intensive sectors there.
Frattini said the legal migration effort required EU states to declare quotas for the migrant workers they needed and that he hoped for progress in ministerial talks next month.
Mali was chosen as the site of the centre ahead of other sub-Saharan countries because it has a national employment agency and experience of bilateral accords, with countries such as France.