Ive seen this happening a lot, a fellow worker with me had the same problem, was assured by my manager that his visa will be taken care of and not to worry and stuff.
6 Months of reassurance and suddenly gets a call for deportation and was basically used without any good salary for those 6 months...

Ask ur manager what will be the max time it will take and if he fails to complete ur papers by that time...then find someone who will !

Whats ur occupation and nationality btw ? and are u aplying in government or private sector ?