Under the agreement between RUPA and the ARU, players were set to receive $12,374 per Test match in 2009 - up from the 2008 fee of $11,875.
RUPA has agreed to a fee of $11,500 for 2009, with the rate expected to return to the pre-agreed figure in 2010.
"The ARU were able to convince us that, like most other industries, there were abnormal financial constraints being imposed on our sport that needed addressing from all key stakeholders including the players themselves," RUPA CEO Tony Dempsey said.
"Furthermore the ARU was able to illustrate to RUPA they were adopting sensible measures to reduce costs.
"The players are key stakeholders who have a vested interest in ensuring the future financial integrity and health of the game.
"They are custodians of the game and so a decision like this when presented with all the facts was sensible.
"Overall the savings to the ARU in terms of the player bill will be over half a million dollars when one also considers there is no longer a need for Australia A player payments."
The ARU is predicting hard times in 2009 as the financial crisis bites into the sporting dollar.