Warren Gatland is currently putting together his team for the 2013 Lions tour of Australia and was keen to add Rowntree and Farrell to his staff.
The pair were only recently confirmed on England coach Stuart Lancaster's team but the RFU says it will be prepared to release them and find alternative arrangements for England's tour of Argentina.
"Our view is that it is still an honour to be asked to be involved with the Lions, we would regard it as such," said Rugby Football Union chief executive Ian Ritchie.
"I don't see it as a negative. I see it very much as a positive. We want to support the Lions, we are one of the shareholders in the Lions, so why wouldn't we?
"Of course it has some difficulties in terms of the summer tour in Argentina but we would deal with that, depending on who it is and how we address it.
"You have to see it as an opportunity. Not only is it an honour but you would believe they would learn a lot in those situations and it gives us an opportunity to broaden our horizons."
Rowntree worked with Gatland as part of Ian McGeechan's coaching set-up on the 2009 Lions tour of South Africa and the former New Zealand coach was impressed with the impact made by Farrell during his short time with England during the Six Nations.
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