In Paris, the French foreign ministry confirmed the sending of the letter in August but denied that it offered a deal with Tehran.
Foreign Ministry spokesman Herve Ladsous said the three European states had called on Iran to make a "strong gesture" by signing an additional protocol to allow surprise visits to suspect sites by international inspectors.
In Vienna, a diplomatic source at a meeting of the UN nuclear watchdog, the International Atomic Energy Agency (IAEA), told AFP however that the letter had proposed increased cooperation, without providing further details.
Iran has said it will only sign the additional protocol to the nuclear Non-Proliferation Treaty (NPT) if it receives transfers of nuclear technology for peaceful purposes.
Washington has said that Iran must unconditionally sign the protocol.
The diplomatic source said the United States was concerned that the letter by Britain, France and Germany would "send a confused signal" to Tehran.
He said Washington had told these three countries that sending the letter was "not the wisest course of action" and "might not be a good path to take."
But he said worries of a split in the Western alliance "came to nought" when the IAEA on September 12 imposed an October 31 deadline on Iraq to prove it is not secretly developing nuclear weapons and to sign the protocol.