The length (Len()) of a field will be numeric.
Try the following:
SELECT a.[FA Ctr], a.[SAP Co], a.[SAP Ctr], a.[GL Co],
IIf([Len([SAP CO])] =3,'0' & [a].[SAP CO], IIf([Len([SAP CO])]=2,'00' & [a].[SAP CO]), IIf([Len([SAP CO])]=1,'000' & [a].[SAP CO]", "[A].[SAP CO]"))) AS Expr3
INTO...