Under new UEFA rules, matches in qualifying for Euro 2016 will be staged every day from Thursday to Tuesday of double-header international weeks.
UEFA introduced the "week of football" to make international matches more attractive for television with only eight to 10 games being played on any one day instead of 20 to 30.
"The thing I'm most concerned about is Thursday," Hodgson, whose side were grouped with San Marino, Lithuania, Estonia, Slovenia and Switzerland at Sunday's draw, said in a television interview with Sky Sports.
"I fear that in our preparation we will have to deal with top (Premier League) matches on Sunday, which means we wouldn't really get to work with the players before the Tuesday.
"I would much rather have Saturday-Tuesday than Thursday- Sunday because I don't think we will be able to persuade the Premier League and Sky Sports to bring the best fixtures to the Saturday and it would mean we get no preparation."
Wales manager Chris Coleman, whose side were drawn in Group B with Bosnia, Belgium, Israel, Cyprus and Andorra, has similar reservations about the new format.
"I think if you're a club manager, and I've been a club manager, you look at that and you're not really going to like that because there is more demand on the players," the former Fulham and Real Sociedad manager told Sky Sports.
"We are very, very careful when the players come with us because we know they're not our players and we have borrowed them effectively like all international managers do.
"We have got to send them back as fit and able as we possibly can."
(Reporting By Michael Hann; editing by Clare Lovell)
