Can I include a 1099 independent contractor on my weekly certified payroll reports?

My company is working on an air force base (in Oklahoma) that requires weekly certified payroll reports. We have 4 employees that I have been doing reports on each week. Last we we hired an independent contractor to do some concrete work that we will be sending a 1099. It is just him and he doesn't have any employees. Do I include him on my payroll reports? If so, how do I do that since he is not an employee and I will not be taking any taxes out?