Her comments come after a deal was struck earlier this month allowing for the US to supply India with nuclear fuel and technology, despite India's refusal to sign the Nuclear Non-Proliferation Treaty.
While Australia supports the treaty, Prime Minister John Howard said only NPT signatories would be permitted to buy Australian uranium.
Dr Rice said that it is an issue that the US should not become involved in.
"I appreciate that the Australian government ... has said that they think the deal itself is a good deal," she told reporters, after meeting with Foreign Minister Alexander Downer.
"I think the issue of whether or not one agrees to participate in fuel supplies is a quite separable issue and is one for the Australians to determine.
"It's not one that is at issue with the United States by any means."
She said India, as a growing world economic power, needs help in meeting its substantial energy needs.
China "must be more transparent"
Earlier, Dr Rice flagged concerns about the rising influence of another world power, China, and said allies need to work together to ensure it is a positive force in the region.
Mr Downer has since tried to soothe Chinese concerns, saying it would be a mistake to try to contain China.
Dr Rice said the US' policy on China has remained the same since the start of the Bush administration, and Beijing needs to be encouraged to be transparent and open, hinting at concerns over its human rights record.
"The growth of the Chinese economy if it's done in a rules-based way, in which China is fully obeying the rules of the global economy, is a very positive development for international growth and for the United States," Dr Rice said.
"We've said we have concerns about the Chinese military build-up, we've told the Chinese they need to be transparent about what their military build-up means."
Dr Rice is in Australia for a three-day visit which will culminate in a trilateral security dialogue involving her, Mr Downer and Japanese Foreign Minister Taro Aso.
On Thursday, she travelled in a 17-car convoy that included an armoured police car, and was shadowed by helicopters.