Those players who were involved in the summer tour of South Africa must undergo a ten-week pre-season conditioning programme, ruling them out of the opening three rounds of the CL.
Munster and Leinster will be the two provinces worst hit by the ruling, losing a total of 19 players between them.
Leinster chief exec Mick Dawson has expressed his anger at the announcement, stating: "We want to have a serious CL, it's our bread and butter competition and I don't think we should be devaluing it.
"I think it's unfair on the competition, unfair on the supporters and unfair on the sponsors."
The move has also angered Welsh and Scottish sides, who now face difficulties marketing ties against under-strength Irish sides.
Llanelli chief exec Stuart Gallacher added: "We are never going to get the league up to Zurich Premiership standard while the Irish refuse to commit to it in the same way as the Welsh and the Scots.
"Their star names are probably only going to be playing in half the league games, so Leinster and Munster will be loathe to agree to qualification for the Heineken Cup being based on the CL.
"Until we get that, it's not going to be a fully blown, meaningful competition."
The IRFU recently denied speculation that top stars like Brian O'Driscoll and Ronan O'Gara would be restricted to playing home ties in the CL.