How much does an employer pay the government for a 1099 on wages paid a 1099 employee?

None. The employer does not have to pay the half of the Social Security Tax or Medicare Tax that they would if you were an employee. The normally also get out of paying Unemployment Taxes, Retirement Benefits, Medical Insurance, and General Liability and Worker's Compensation Insurance Premiums. The IRS is really cracking down on employers who try to call their employees subcontractors.