The data-collection program, in which the National Security Agency (NSA) sweeps up vast amounts of Americans' telephone records and business information, was exposed two years ago by former NSA contractor Edward Snowden, who is now a fugitive in Russia.
The vote against the extension came after the Senate narrowly blocked the "USA Freedom Act," a bill that would end the bulk telephone data collection and replace it with a more targeted program.
That vote was 57-42, just short of the 60 needed.
President Barack Obama's administration had pushed hard for the Freedom Act. The House of Representatives backed it by an overwhelming margin, with strong support from Republicans and Democrats, on May 13.
Backers of the bill in the House, including Representative Bob Goodlatte, R-Va., the chairman of the Judiciary Committee, said the Senate's failure to act risked the Patriot Act provisions' expiration before the House returns to Washington late on June 1.
"The Senate has failed to make the important reforms necessary, jeopardizing Americans’ civil liberties and our national security," the committee said in a statement.
Two other surveillance authorities would expire along with the government’s bulk collection of telephone data. One makes it easier for the FBI to track "lone wolf" terrorism suspects who have no connection to a foreign power, and another allows the government to eavesdrop on suspects who continuously discard their cellphones in an effort to avoid surveillance.
McConnell, R-Ky., proposed short extensions, ending with one lasting only until June 2, to keep the Patriot Act provisions from expiring. However, they were blocked by Sen. Rand Paul, R-Ky., and Sen. Martin Heinrich, D-N.M.
The Patriot Act was passed to increase national security in the wake of the Sept. 11, 2001, attacks. Backers of the Freedom Act argued that it provided national security protections while eliminating provisions of the Patriot Act that raised privacy concerns.
Paul, a 2016 Republican presidential candidate and vocal advocate for privacy rights, led more than 10 hours of speeches against the Patriot Act on Wednesday.