The piece was in response to an op-ed from Sen. Barack Obama that was published in the paper last week.
In an e-mail to the McCain campaign, Opinion Page Editor David Shipley said he could not accept the piece as written, but would be "pleased, though, to look at another draft."
"Let me suggest an approach," he wrote Friday. "The Obama piece worked for me because it offered new information (it appeared before his speech); while Senator Obama discussed Senator McCain, he also went into detail about his own plans. It would be terrific to have an article from Senator McCain that mirrors Senator Obama's piece." Read McCain's rejected piece
In a statement released Monday, The New York Times said it is "standard procedure on our Op-Ed page, and that of other newspapers, to go back and forth with an author on his or her submission."
"We look forward to publishing Senator McCain's views in our paper just as we have in the past. We have published at least seven Op-Ed pieces by Senator McCain since 1996. The New York Times endorsed Senator McCain as the Republican candidate in the presidential primaries. We take his views very seriously," the statement said.
McCain's rejected op-ed was a lengthy critique of Obama's positions on Iraq policy, particularly his view of the surge.
McCain's rejected op-ed piece
Obama: Iraq timetable 'an enormous opportunity'
"Senator Obama seems to have learned nothing from recent history," wrote McCain, criticizing Obama's call for an early withdrawal timeline. "I find it ironic that he is emulating the worst mistake of the Bush administration by waving the 'Mission Accomplished' banner prematurely." Watch why the piece was rejected »
Obama's July 14 essay had taken shots at McCain for not further encouraging the Iraqi government to take control of the country.
"Instead of seizing the moment and encouraging Iraqis to step up, the Bush administration and Senator McCain are refusing to embrace this...