My question is why is your pastor getting a 1099 instead of a W-2?
but beside that question... (from IRS Pub 1828 and this site)
In order to qualify for the exclusion from federal income tax, two very important conditions must be satisfied:
•The housing allowance must be board approved before it was paid (A housing allowance is NEVER retroactive)
•The minister actually spent the allowance on eligible housing expenses during the year
Your church must make sure the amount they are going to pay as an allowance for housing is determined before it is paid. It should be included in a board approved resolution and properly documented in the church records. Most of the time, it is reviewed and adjusted before the beginning of each new budget year.
you might want to look to the left and scroll down to the Clergy/Minister section :-)
also a good set of IRS Pubs for churches are the 15 series