Locked in a tight race, Nevada Sen. Harry Reid became the highest profile Democrat to respond to Obama, who last week backed the right for the developers to build a mosque near ground zero.
Since his comments Friday, the Democratic president and his aides have worked to explain the statement, which drew criticism from Republicans and Democrats alike.
"The First Amendment protects freedom of religion," said Jim Manley, a Reid spokesman. "Senator Reid respects that, but thinks that the mosque should be built some place else."
Critics have said the location of the mosque is insensitive because the terrorists who struck were Islamic extremists. The plans call for a $100 million Islamic center two blocks from where almost 3,000 people perished when hijacked jetliners slammed into the World Trade Center towers on Sept. 11, 2001.
"As the president said on Friday night, he respects that Americans of all political persuasions will have different opinions on this issue," White House spokesman Bill Burton said, commenting on Reid's position. "That is a strength in our country and in the Democratic Party. Senator Reid is a fiercely independent individual and the president believes that is one of his strengths as a leader."
Reid is in a close campaign for re-election. A spokesman for Republican Sharron Angle, Reid's opponent, said Muslims have the right to worship anywhere, but Obama's support for construction of the mosque at ground zero "ignored the wishes of the American people, this time at the expense of victims of 9/11 and their families."
Spokesman Jarrod Agen argued that the families consider the mosque at the World Trade Center site to be an "affront to the memories of their loved ones." He called on Reid to respond to Obama's comments.
On Friday, Obama used an annual dinner at the White House celebrating the Islamic holy month of Ramadan to weigh in on a controversy that grabbed New York and the nation.
"As a citizen, and as president, I believe that Muslims have the same right to practice their religion as everyone else in this country," Obama said.
"That includes the right to build a place of worship and a community center on private property in lower Manhattan, in accordance with local laws and ordinances," he said.
While insisting that the place where the twin towers once stood was indeed "hallowed ground," Obama said that the proper way to honor it was to apply American values at the nearby property.
In days since, White House aides have worked to dampen the political power behind the president's words.
"I can't speak to the politics of what the Republicans are doing," Burton told reporters traveling with Obama to Wisconsin on Monday.
But he said Obama "felt it was his obligation as president to address this."