Under current law, government officials only need a subpoena, issued without a judge's approval, to compel Internet companies to turn over their users' private messages.
The Senate Judiciary Committee approved legislation earlier this year that would set a warrant-standard for all online messages. Lawmakers in the House are working on companion legislation.
Some administration officials have warned that the warrant requirement could impede civil regulatory investigations in areas such as antitrust, civil rights, financial fraud and environmental protection. Warrants are only available in criminal cases.
But privacy advocates argue that regulators can still obtain relevant information by directly subpoenaing the individuals or companies who are under investigation. They say defendants and their lawyers should be making decisions about when to withhold irrelevant or privileged documents, not a third-party Internet provider who isn't involved in a case.
Digital 4th, a coalition of civil liberties groups favoring tougher privacy protections for online information, called Yoder's amendment a "huge step forward."
"The overwhelming vote, on a bipartisan basis, shows that Congress supports updating our laws to make it clear that the protections of the Fourth Amendment also apply to electronic data," the group said in a statement.
—Updated at 11:03 a.m.