Hi,
I came on L1 from india,My employer stated for first 90 days he will not run the payroll but will pay perdim basis for first 90 days(Non taxiable).From the 91st day he wanted to run the payroll for me...
My Query :
1.If my employer send me back after completing 90 days will I get effected for not paying tax for the 90days stay?
2. Is that OK my employer runs payroll after 91st day or we will get any issues ?

It would be great help if any one guide me in this.

Thanks,
Saibabu Kolli

You are a contractor for those 90 days and do owe taxes. He gives you a 1099 MISC form with the amount, and the IRS gets a copy.
After you become an employee, taxes are deducted from each paycheck. You still file a tax return, both types of income on one return, if in the same year.
I see no problem depending on the time limit of your visa.