Elmendorf told members of the Senate Budget Committee that the bills don't contain the kind of fundamental changes necessary to reduce federal spending.
"On the contrary," he said, "the legislation significantly expands the federal responsibility for health-care costs."
The CBO is a nonpartisan office responsible for evaluating the costs of legislation, and its support could make or break the prospects of a health care reform bill.
Elmendorf was speaking of draft legislation unveiled Tuesday by House Speaker Nancy Pelosi, which is currently being marked up in three House committees, as well as a bill passed by the Senate health committee Wednesday.
Both of those bills would create a public health insurance option to compete with private insurers, and would subsidize lower-income Americans to help them afford health insurance.
Asked what would be necessary to reign in healthcare costs. Elmendorf suggested a tax on employer-provided health benefits -- something congressional Democratic leaders and President Barack Obama have spoken out against. None of the House or Senate legislation unveiled so far has contained an employer-benefit tax.
But Sen. Max Baucus, D-Mont., chairman of the Senate Finance Committee, has been a proponent of the idea. His committee has yet to come to an agreement on draft legislation, although he said Thursday that bipartisan negotiators on his committee were nearing an agreement.
Sen. Richard Durbin, D- Ill., the assistant majority leader, expressed frustration with the CBO's analysis of their health care reform legislation.
"It's been really hard to work with them, and I want to continue to, but there's some frustration being felt," Durbin said, according to the Wall Street Journal.
And Senate Majority Leader Harry Reid, D-Nev., jokingly suggested that Elmendorf should run for Congress if he wants to promote an employer-benefits tax.