WASHINGTON—The Treasury Department has taken down a 2012 economic analysis that contradicts Secretary Steven Mnuchin’s argument that workers would benefit the most from a corporate income tax cut.

The 2012 paper from the Office of Tax Analysis found that workers pay 18% of the corporate tax while owners of capital pay 82%. That is a breakdown in line with many economists’ views and close to estimates from the nonpartisan Joint Committee on Taxation and Congressional Budget Office.

The JCT, which will evaluate tax bills in Congress, estimates that capital bears 75% of the long-run corporate-tax burden, with labor paying the rest.

But Mr. Mnuchin has been arguing the opposite, citing other papers that attribute more of the burden to labor. The point is central to Mr. Mnuchin’s argument that workers would benefit from the corporate tax cut the administration is proposing, and switching that assumption would significantly alter the estimates of who would benefit from the Republican tax policy framework released on Wednesday.

Asked about the paper’s disappearance, a Treasury spokeswoman responded Thursday: “The paper was a dated staff analysis from the previous administration. It does not represent our current thinking and analysis.”