Pieth's comments could fuel longstanding tension with UEFA, which questioned his integrity earlier Monday.
Though Pieth's FIFA consultancy work ended last year " with key proposals rejected " he was brought into the election campaign debate after a German magazine's weekend report based on his exchanges with FIFA's legal director.
Der Spiegel claimed Pieth gave into FIFA's request and removed criticism of Blatter in their summary report published last April.
UEFA, often cited by Pieth and his colleagues for blocking the FIFA reform program, hit back saying the leaked exchanges showed the advisory panel had been "anything but independent."
Pieth confirmed to AP that his 15-page document summarizing two years of work had been submitted to FIFA in February 2014 before publication.
"Anything else would be unprofessional," he insisted, adding that his panel went along with four of 37 suggested changes. Two involved minor fact-checking details.
Two paragraphs were deleted which had speculated on Blatter's awareness of then-colleagues taking kickbacks from World Cup commercial deals before the 2001 financial collapse of FIFA's marketing partner ISL.
A FIFA ethics investigation concluded in April 2013 that Blatter was "clumsy" but not guilty of misconduct in the affair. In 1997, as FIFA's chief executive, he sent back to ISL's bank a 1.5 million Swiss francs (then $1 million) payment which arrived at FIFA for then-president Joao Havelange.
"Our role was not to investigate Blatter. Our role was what should happen in the long run with the institution," Pieth recalled of his panel agreeing to remove the Blatter passages. "Beating up on him passes the wrong message.
"If you concentrate everything on Blatter you say 'Blatter is the problem and as soon as he goes everything is fine,'" he said. "And that is not what we wanted to say."
Pieth said his group's thinking one year ago was: "This institution has systemic problems and Platini coming in doesn't change a bit."
UEFA President Michel Platini was then viewed as election favorite if Blatter chose not to stand, but last August opted out of the contest.
Pieth suggested the leak to Der Spiegel was timed to undermine his panel after some members recently called on the FIFA president to end his 17-year reign.
"There is a certain logic because three of us were turning against Blatter," said Pieth, identifying the critics as himself, Peter Goldsmith, a former British government attorney general, and Michael Hershman, a former Senate Watergate Committee investigator.
Still, UEFA tried to align Pieth with Blatter on Monday.
"UEFA has always wondered why it was criticized by Mr. Pieth and wrongly accused of blocking FIFA reforms. Now we understand why and where it all came from," its statement said.
Pieth offered a second theory for the leaked emails at the start of presidential campaigning.
"It's possible that some people within FIFA management wanted their last go at Blatter," the former United Nations investigator said. "It's kind of hopeless because Blatter will get his votes."