Cook Political Report on Friday said Clinton had 65,250,267 votes compared to Trump's 62,686,000 votes.
Clinton's victory in the popular vote has generated criticism of the United States' Electoral College system, which Trump won 306-232. Efforts to conduct recounts are occurring in Michigan, Pennsylvania and Wisconsin.
"Voters should not risk having the Electoral College door knocked off its hinges all because a 1 percent candidate is dissatisfied with the election's outcome," the objection states. "Given her tiny vote total, Stein does not and could not possibly allege a good faith belief that she may have won the state of Michigan."
Trump on Sunday lashed out at the recount efforts. He said millions voted illegally but offered no proof to substantiate his claim.
"In addition to winning the Electoral College in a landslide, I won the popular vote if you deduct the millions of people who voted illegally," Trump tweeted.
Clinton's loss is the fifth time in U.S. history a candidate who won the popular vote did not assume the presidency. The last time was in 2000, when former Vice President Al Gore defeated then-Texas Gov. George W. Bush in the popular vote, but lost the recount in Florida -- giving Bush the needed electoral votes to win the executive branch.
Since his election victory, Trump has defended the Electoral College, despite calling the system a "disaster for a democracy" in 2012.