England's players all took anti-malaria tablets Malarone on Tuesday morning at breakfast ahead of their trip to face Italy in the jungle city of Manaus on Saturday.
One in 10 people can experience side-effects like stomach cramps, sickness and dizziness after taking the pills but Hodgson felt he was left with no other option.
But, after consulting FIFA's chief medical officer, Professor Dr. Jiri Dvorak, England have decided not to take yellow fever jabs.
He said: "As far as I'm concerned, I've got to go with medical opinion and if the doctors are telling me that when we go to Manaus the players must take malaria tablets, whether it has side-effects or not, what do I do?
"I can't turn around and say 'we will not take malaria tablets", because the bottom line is better stomach cramps or whatever it is for one player in 10 than have someone contract malaria because that would be unthinkable."
Interestingly Hodgson did not take any anti-malaria drugs before a trip to Manaus last year, but the Football Association has confirmed he will do so this time around.
"I went to Manaus and I didn't take any for the two days I spent there," he said.
"That might just be something to do with the fact that I'm not a football player."
Hodgson believes his team have a better chance of overcoming Italy at the weekend than two years ago, when they lost to Cesare Prandelli's men at Euro 2012 on penalties after a 0-0 draw in Kiev.
"We have more options [than at Euro 2012]," he said.
"We certainly have more athleticism, we have more pace, more mobility. We have a lot of technical players."
This time the match cannot go to penalties, but that did not stop the squad practising spot-kicks at Urca on Tuesday morning.
Speaking before the session began, Hodgson said: "Today we will have a little penalty practice at the end of the session but we haven't got down to thinking who (our five takers) will be."