If you have registered using your warehouse excise ID instead of warehousekeeper excise ID you will need to de-enrol from the service.
To de-enrol for EMCS you need to do the following:
login to the HMRC portal at www.online.hmrc.gov.uk
follow the 'Your account' link from the left hand menu on the 'Your HMRC services' page
follow the 'Remove services' link
follow the 'Remove service' link next to Excise Movement & Control System
confirm the removal by clicking on the 'Yes' button
You can now re-enrol using your warehousekeeper excise ID by following the EMCS 'Enrol for service' link on the 'Your HMRC services' page.