The IPL insists the two left-handers will represent their Indian franchise, the Chennai Super Kings, in the mooted Champions League Twenty20 tournament, due to be played in September-October.
But the tournament - which will pit the best Twenty20 teams from Australia, India, South Africa and England against each other to determine the world's best domestic side - will clash with the start of the keenly-anticipated Australia's Test tour of India.
Ricky Ponting's side is scheduled to play a four-day tour match from Octr 2-5 - their only warm-up clash before the first Test - at the same time as the Champions League is to be staged.
IS Bindra, a member of the IPL governing council, admitted the two Australians faced a scheduling clash, but said Hayden and Hussey would be playing for their club and not their country.
"Hussey and Hayden, the two key players facing a clash of dates, will play for the Chennai team," Bindra told the Cricinfo website.
CA spokesman Peter Young said there was a lot of uncertainty around the planned tournament, and that representatives from the four boards would get together to discuss the sticking points.
But Young said CA was keen to have its players represent Australia first.
"Our position was always that international duties would always take precedence and the IPL always agreed with that," he said.
The IPL's clout also means Chennai can take precedence in getting Hussey from Western Australia, provided they pay the Warriors a relieving fee.
Although the details are yet to be finalised, administrators hope to stage the Champions League in the short window between the Champions Trophy in Pakistan and the Australia-India Test series.
Australia will be represented by Victoria and Western Australia, India by Shane Warne's Rajasthan Royals and Chennai and South Africa by the Titans and Kwazulu Natal Dolphins.
England's two sides will be determined by their domestic Twenty20 tournament.