It is not unusual for an employer to try to treat an employee as a contractor, in order to avoid paying payroll taxes. If you are an employee, then your employee has to pay 1/2 of the payroll taxes (7.65% of your salary), but if you are a contractor, then you have to pay all of your payroll tax (called "self-employment taxes") which is 15.3% of your net profit from your business (your 1099-MISC less any valid expenses).
If you want to cause some trouble for your employer (who may not be happy about it), see this IRS page, especially the section under "Misclassified Workers Can File Social Security Tax Form".
A more peaceful way out is to accept (for the time being) that you are being treated as a contractor, and ask your boss to increase your compensation to cover your cost of the payroll tax and any benefits like health insurance that he gives to employees. And then ask him when he is going to convert you to an employee per the IRS definition.
Ever wonder why consultants seem to charge so much per hour? This is why - they have to cover all their own costs.
Oh, sorry, to enter your 1099-MISC, do a Search for 1099-MISC and click on the jump-to result.
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