McCain made the comment a day after Palin stunned the political world by announcing she is stepping down with 18 months left in her term.
McCain had plucked Palin from obscurity to make her his vice presidential running mate in last year's presidential campaign won by Democrat Barack Obama.
"I have the greatest respect and affection for Sarah, Todd, and their family. I was deeply honored to have her as my running mate and believe she will continue to play an important leadership role in the Republican Party and our nation," McCain said in a statement e-mailed to Reuters.
But Alaska's Republican Senator Lisa Murkowski issued a statement saying, "I am deeply disappointed that the Governor has decided to abandon the State and her constituents before her term has concluded."
Palin defeated Murkowski's father, then-Governor Frank Murkowski, in the 2006 Republican primary for governor.
A polarizing figure who is mainly popular among conservatives, Palin has often been considered a possible contender for the Republican presidential nomination in 2012.
Her decision, announced in a rambling, disjointed statement in her home town of Wasilla, Alaska, fueled speculation that she might be seeking to position herself for a run.
But some commentators said it was a strange move for one with presidential ambitions, opening her to potential criticism that she quit her post to pursue a personal agenda.
In her statement, Palin referred to a series of ethics probes into her conduct as governor and previously as mayor of Wasilla, all of which she said lacked merit.
"My staff and I spend most of our day dealing with this instead of progressing our state now," Palin said. "This isn't what anyone had in mind for Alaska."
McCain's statement of support came after some of his political aides from last year's campaign outlined their grievances with her in an article in the current issue of Vanity Fair magazine.
Palin, 45, initially boosted the McCain ticket, especially after delivering a masterly speech at the Republican National Convention introducing herself as a "hockey mom."
But her approval ratings plummeted following a disastrous series of TV interviews and many voters wound up concluding she lacked the qualifications to be vice president.
Public ridicule continued in the eight months since the election. She recently engaged in an angry public dispute with comedian David Letterman over jokes Letterman made about her and Palin's daughter, Bristol, on his CBS show, "The Late Show with David Letterman."
Some prominent Republicans do not blame her for deciding to step down.
"I'm sure she felt that the only way to end the ridicule that was attempting to tear her family apart was for her to get off the stage for now," said Dana Perino, who was press secretary for President George W. Bush.
Palin is said to have a book in the works. In addition, Nick Ayers, executive director of the Republican Governors Association, told Fox News on Friday that Plain wants to expand her role in the national party.
"Part of her decision is she wants to spend more time campaigning for candidates," he said.
That could be a welcome role for her in some parts of the Republican Party, which has suffered devastating losses in elections in 2006 and 2008 and is seeking ways -- and new leaders -- to help it rebuild.
Perino said that while the "2008 election and the aftermath of it would be something very hard to overcome politically" for Palin, she could be a powerful symbol for the party as it tries to encourage more women to run for office.