The senators on Wednesday, March 15, during a plenary unanimously passed a motion to issue the warrant
The Senate decision came after Ali failed to make an appearance before the Red Chamber today.
He had in a letter told the Senate that he (Ali) would not be able to appear before it because he was bereaved.
The customs boss was told by the senate that he (Ali) must appear before them dressed in a custom's uniform.
However, Ali, a retired Nigerian army colonel in his response said will not wear uniform as he was only appointed to work and reform the Nigeria Customs Service.
Ali also said he cannot be mandated to wear customs' 'Khaki' as a retired senior officer of the Nigerian army.
However,a former custom boss Bello Haliru debunked such claim.
In an interview he said that wearing uniform as a comptroller general is part of the service's regulation.
In a related event, protesters on Wednesday afternoon, hit the streets of Anambra state over the actions of the comptroller general of customs.
The protesters in their scores demanded the removal of Ali with immediate effect.