The IRB are taking steps to avoid a repeat of the scenario that sees England face New Zealand in next summer's first Test with a weakened team.
England's three-Test series begins on 7 June, just seven days after the Aviva Premiership final is staged at Twickenham.
The proximity of the dates means head coach Lancaster is resigned to being unable to field his strongest side until the second Test on 14 June.
IRB chief executive Brett Gosper regrets the confusion that arose over when the international window opens and hopes to prevent it from happening again.
"It's unfortunate, but it's the product of a crowded season," said Gosper. "These calendars were decided some years ago and everyone was involved in that.
"I believe there was a little bit of confusion on behalf of some of the unions as to what the beginning of the window was in June.
"It's unfortunate that the two unions couldn't find a solution to the problem and it does look like England won't take a full strength side.
"We tried to move it but there were broadcast and planning elements in place that meant we couldn't.
"We're looking at the windows at the moment to see if we can find a better balanced calendar. It's a very crowded season."