Hitzfeld, speaking on Germany's SWR radio, blamed commercial interests for the controversial scheduling.
"In Salvador it's very hot, Manaus is much worse because you are playing in a humid, tropical climate, with 95 percent humidity, and a temperature between 30 and 40 Celsius," he said.
"I find it almost irresponsible that one has to play football in such a place, in the middle of the jungle, in the middle of the Amazon region."
The German added: "I think the commercial side has taken precedence and I am not in agreement with FIFA.
"Brazil is a big country and you have to fly for five hours from ..... Salvador to Manaus and that is also a big strain for us.
"We have some meetings in the next few weeks with sport scientists, with doctors and physiotherapists, we have to assess this intensively and prepare ourselves accordingly."
Teams at the World Cup will have to travel around the country for their group games, rather than remaining in single venue, a decision which means some will have to fly thousands of kilometres between matches.
Organisers have also been criticised for scheduling some matches at 1300 local time in tropical venues, with the world players' union FIFPro among those who have complained.
Switzerland start their campaign against Ecuador in Brasilia on June 15, where humidity can drop as low as 20 percent.
They then play in tropical Salvador against France five days later before taking on Honduras in Manaus on June 25.
(Writing by Brian Homewood in Berne)
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