"I am surprised by Mr Garcia's decision.," Blatter said in a statement released following the decision of the US lawyer to quit as head of Fifa's ethics committee investigatory committee.
"The work of the Ethics Committee will nonetheless continue."
The Fifa president added the inquiry into the Qatar and Russia World Cups "will be a central part of the discussions" at a Fifa executive committee meeting in Marrakech, Morocco, on Thursday and Friday.
Jérôme Champagne, a former Fifa official who has said he will stand against Blatter for the Fifa presidency next year, called Garcia's resignation "a step backwards" for the governing body.
"We needed to know what happened before and after the December 2nd 2010 vote," Champagne said in a statement..
"Today more than ever we need to know," he said.
"When will the facts be known fully, transparently and above all without suspicion?"