Hodgson, speaking after England were handed a straightforward draw for Euro 2016 in Group E alongside Switzerland, Slovenia, Estonia, Lithuania and San Marino, said playing matches on a Thursday would mean having just one day to train with the squad.
Euro 2016 qualifiers will see UEFA's 'week of football' idea put into practice, with matches taking place every day from the Thursday to Tuesday of double-header international weeks.
England's first home match of the campaign is on a Thursday, against San Marino on October 9, and Hodgson, who also admitted the Football Association faces a tough task to sell out Wembley for the low-profile opponents, said: "It will affect the national teams.
"One of the major problems for us could be a Thursday game if the Super Sunday has four of our best teams taking part, taking as many as seven or eight of our first XI players.
"That means Monday is a write-off, Tuesday for some of the older players will be a write-off because they need a two-day recovery and don't train two days after a game.
"That would mean we have one day, the day before the game, to prepare the team.
"The clubs will be happier because it used to be two weeks for the national teams in these breaks.
"That got knocked down to 10 days. Then it was knocked down to nine days. Now it's seven or eight days, so the clubs, I would think, are rubbing their hands all the time because they get the players back quicker all the time."
Scotland and the Republic of Ireland were drawn in Group G along with Germany, Poland and Georgia, as well as UEFA's newest member Gibraltar.
Irish boss Martin O'Neill said: "I think it's the toughest group but it's an exciting one.
"We have got Scotland, we have Poland who we have played in a recent friendly and whose recent efforts (against England) at Wembley were not too bad at all."
It will bring O'Neill face to face with his fellow ex-Celtic manager Gordon Strachan, who claimed it was a "terrific draw" - while other groups appeared "mundane".
Wales' chances of qualifying look equally difficult, in Group B with Bosnia-Herzegovina, Belgium, Israel, Cyprus and Andorra.
Northern Ireland were drawn in Group F with Greece, Hungary, Romania, Finland and the Faroe Islands.
The top two in each group will qualify for the 24-team final tournament along with hosts France. The best third-placed team will also qualify, with the eight other third-placed sides playing off for the remaining four spots.