Mini is to withdraw its financial support for its works team - WRC Team Mini Portugal - at the end of this season.
The team's drivers Chris Atkinson and Paulo Nobre face an uncertain future with the Motorsport Italia-run squad following an announcement by Dr Key Segler, senior vice-president of Mini business coordination and brand management, on Friday.
Segler said: "Mini will abandon its works involvement in the WRC at the end of the 2012 season."
FIA World Rally Championship regulations stated that Mini had to contest every round of the season for its WRC machine to fulfil its homologation obligations.
With this to be completed by the end of the season, the budget for running the works cars in 2013 has been withdrawn.
Segler added: "By the end of the season WRC Team Mini Portugal will have competed in every rally in 2012.
"As such, in accordance with FIA regulations, we will have achieved the WRC homologation for the Mini John Cooper Works.
"In doing so, we would have achieved the prerequisites to allow those interested to continue to run the car in the WRC on a customer rallying basis.
"In a very difficult commercial environment, Mini has played an active role in ensuring that friends of the Mini brand can continue to participate in motorsport.
"As such, the Mini family is retaining its presence on various international platforms and getting even closer to its customers.
"We would like to see the Mini John Cooper Works WRC continue to run competitively in WRC and other championships.
"We would like to thank Prodrive, WRC Team Mini Portugal and our partners for the good cooperation, and wish all drivers, teams and customers a successful future in rallying."
While Mini's decision has a significant impact on Motorsport Italia's 2013 plans, it does not affect Prodrive's participation in next year's world championship.
Segler added: "BMW Motorsport will continue to further develop the 1.6-litre turbo engine in conjunction with Prodrive."
Prodrive's business development director Richard Taylor said the Banbury firm was already looking forward to next season.
Taylor, whose Prodrive team has clinched all three of the Mini's podium spots on WRC rounds, said: "We understand Mini's decision and in the current challenging economic climate it was not unexpected.
"It is however good news that Mini remains enthusiastic about the WRC and wishes to see Mini rally cars continuing to run competitively in the WRC and other championships.
"We look forward to continuing to work with Mini and BMW Motorsport to maximise the performance of both WRC and S2000 Minis on behalf of our mutual customers and our own WRC team."